Starting phenix.real_space_refine on Sun Nov 17 11:22:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn0_40608/11_2024/8sn0_40608.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn0_40608/11_2024/8sn0_40608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn0_40608/11_2024/8sn0_40608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn0_40608/11_2024/8sn0_40608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn0_40608/11_2024/8sn0_40608.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn0_40608/11_2024/8sn0_40608.cif" } resolution = 3.2 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= 0.120 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 32 5.16 5 C 7886 2.51 5 N 2605 2.21 5 O 3170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13989 Number of models: 1 Model: "" Number of chains: 13 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: "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 33.133 68.087 45.798 1.00 30.76 S ATOM 12446 SG CYS K 51 33.688 64.517 44.566 1.00 32.93 S ATOM 12470 SG CYS K 54 33.196 67.190 42.087 1.00 33.86 S ATOM 12187 SG CYS K 16 23.428 61.844 52.457 1.00 53.78 S ATOM 12205 SG CYS K 19 21.803 59.154 54.554 1.00 59.20 S ATOM 12335 SG CYS K 36 24.773 60.893 56.009 1.00 41.49 S ATOM 12357 SG CYS K 39 25.149 58.405 53.280 1.00 41.62 S Time building chain proxies: 8.58, per 1000 atoms: 0.61 Number of scatterers: 13989 At special positions: 0 Unit cell: (108.896, 128.816, 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 32 16.00 P 294 15.00 O 3170 8.00 N 2605 7.00 C 7886 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: 3.69 Conformation dependent library (CDL) restraints added in 1.4 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 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " 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 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 12 sheets defined 64.5% alpha, 4.7% beta 136 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 6.73 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.548A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.590A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.021A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.873A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.724A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.701A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.765A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.588A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.996A pdb=" N SER D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.947A 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 105 through 123 removed outlier: 3.688A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.618A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.537A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.553A 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: 4.221A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.630A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) 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 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.524A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.684A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 Processing helix chain 'K' and resid 58 through 68 removed outlier: 3.818A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 removed outlier: 3.862A pdb=" N LYS K 82 " --> pdb=" O THR K 78 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS K 83 " --> pdb=" O ILE K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 91 removed outlier: 3.535A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG K 91 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.582A pdb=" N ALA L 107 " --> pdb=" O LEU L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.516A pdb=" N ALA L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 145 removed outlier: 3.672A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG L 136 " --> pdb=" O ASP L 132 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE L 137 " --> pdb=" O LYS L 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.995A 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 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.205A 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 'C' and resid 100 through 102 removed outlier: 6.635A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.261A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.739A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25 457 hydrogen bonds defined for protein. 1354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2898 1.33 - 1.45: 4518 1.45 - 1.57: 6805 1.57 - 1.69: 586 1.69 - 1.81: 47 Bond restraints: 14854 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.72e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" C3' DA J -73 " pdb=" C2' DA J -73 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.11e+00 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 8.66e-01 bond pdb=" CG LEU E 109 " pdb=" CD1 LEU E 109 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.18e-01 ... (remaining 14849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 20925 1.76 - 3.52: 388 3.52 - 5.27: 20 5.27 - 7.03: 3 7.03 - 8.79: 2 Bond angle restraints: 21338 Sorted by residual: angle pdb=" CB ARG L 139 " pdb=" CG ARG L 139 " pdb=" CD ARG L 139 " ideal model delta sigma weight residual 111.30 120.09 -8.79 2.30e+00 1.89e-01 1.46e+01 angle pdb=" N VAL E 46 " pdb=" CA VAL E 46 " pdb=" C VAL E 46 " ideal model delta sigma weight residual 113.39 108.14 5.25 1.47e+00 4.63e-01 1.28e+01 angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 122.82 126.95 -4.13 1.42e+00 4.96e-01 8.46e+00 angle pdb=" N GLN L 143 " pdb=" CA GLN L 143 " pdb=" CB GLN L 143 " ideal model delta sigma weight residual 110.28 114.54 -4.26 1.55e+00 4.16e-01 7.57e+00 angle pdb=" CA VAL E 46 " pdb=" C VAL E 46 " pdb=" N ALA E 47 " ideal model delta sigma weight residual 118.55 116.54 2.01 8.60e-01 1.35e+00 5.46e+00 ... (remaining 21333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 6809 35.27 - 70.54: 1378 70.54 - 105.81: 26 105.81 - 141.08: 0 141.08 - 176.35: 2 Dihedral angle restraints: 8215 sinusoidal: 5297 harmonic: 2918 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 220.00 43.65 176.35 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 66.81 153.19 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" CA LYS K 46 " pdb=" C LYS K 46 " pdb=" N ALA K 47 " pdb=" CA ALA K 47 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 8212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1592 0.030 - 0.060: 598 0.060 - 0.089: 159 0.089 - 0.119: 55 0.119 - 0.149: 13 Chirality restraints: 2417 Sorted by residual: chirality pdb=" CA ARG L 139 " pdb=" N ARG L 139 " pdb=" C ARG L 139 " pdb=" CB ARG L 139 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.54e-01 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 2.37 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA VAL K 27 " pdb=" N VAL K 27 " pdb=" C VAL K 27 " pdb=" CB VAL K 27 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 2414 not shown) Planarity restraints: 1686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO D 103 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR K 84 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO K 85 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO K 85 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO K 85 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.025 2.00e-02 2.50e+03 1.04e-02 3.24e+00 pdb=" N9 DG I 47 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.002 2.00e-02 2.50e+03 ... (remaining 1683 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1875 2.76 - 3.47: 17259 3.47 - 4.19: 37955 4.19 - 4.90: 59168 Nonbonded interactions: 116259 Sorted by model distance: nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.331 3.350 nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.331 3.350 nonbonded pdb=" O ARG L 139 " pdb=" OG1 THR L 142 " model vdw 2.173 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.215 2.496 nonbonded pdb=" OE2 GLU C 61 " pdb=" OG SER K 60 " model vdw 2.225 3.040 ... (remaining 116254 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 40.340 Find NCS groups from input model: 0.330 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 0.039 14854 Z= 0.201 Angle : 0.558 8.792 21338 Z= 0.331 Chirality : 0.035 0.149 2417 Planarity : 0.005 0.055 1686 Dihedral : 26.424 176.347 6329 Min Nonbonded Distance : 1.331 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.04 (0.27), residues: 982 helix: 1.58 (0.21), residues: 630 sheet: 0.45 (0.99), residues: 24 loop : -1.05 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 141 HIS 0.006 0.001 HIS C 31 PHE 0.008 0.001 PHE B 61 TYR 0.021 0.001 TYR L 134 ARG 0.012 0.001 ARG L 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9480 (p) cc_final: 0.9273 (p) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.3818 time to fit residues: 52.0998 Evaluate side-chains 92 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS H 47 GLN L 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14854 Z= 0.292 Angle : 0.589 10.011 21338 Z= 0.344 Chirality : 0.038 0.155 2417 Planarity : 0.005 0.054 1686 Dihedral : 29.490 176.168 4329 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.59 % Allowed : 7.03 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.10 (0.26), residues: 982 helix: 1.66 (0.21), residues: 635 sheet: 0.56 (1.00), residues: 24 loop : -1.15 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 61 HIS 0.007 0.001 HIS C 31 PHE 0.010 0.002 PHE B 61 TYR 0.026 0.002 TYR L 134 ARG 0.004 0.000 ARG L 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9521 (p) cc_final: 0.9319 (p) REVERT: A 120 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7918 (mtt) outliers start: 5 outliers final: 4 residues processed: 97 average time/residue: 0.3736 time to fit residues: 49.3128 Evaluate side-chains 94 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14854 Z= 0.322 Angle : 0.599 10.415 21338 Z= 0.348 Chirality : 0.039 0.149 2417 Planarity : 0.005 0.053 1686 Dihedral : 29.640 175.924 4329 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.29 % Allowed : 10.32 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.10 (0.26), residues: 982 helix: 1.69 (0.21), residues: 634 sheet: 0.57 (0.99), residues: 24 loop : -1.22 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 61 HIS 0.006 0.001 HIS A 113 PHE 0.011 0.002 PHE B 61 TYR 0.026 0.002 TYR L 134 ARG 0.004 0.000 ARG L 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9531 (p) cc_final: 0.9325 (p) REVERT: A 120 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7935 (mtt) outliers start: 11 outliers final: 9 residues processed: 97 average time/residue: 0.3468 time to fit residues: 45.8691 Evaluate side-chains 98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 73 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 4.9990 chunk 57 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 117 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14854 Z= 0.188 Angle : 0.552 9.268 21338 Z= 0.327 Chirality : 0.036 0.134 2417 Planarity : 0.004 0.049 1686 Dihedral : 29.546 175.860 4329 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.82 % Allowed : 11.14 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.44 (0.27), residues: 982 helix: 1.95 (0.21), residues: 635 sheet: 0.48 (0.98), residues: 24 loop : -1.07 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 61 HIS 0.004 0.001 HIS C 31 PHE 0.008 0.001 PHE B 61 TYR 0.026 0.001 TYR L 134 ARG 0.003 0.000 ARG L 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9518 (p) cc_final: 0.9309 (p) REVERT: A 120 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7891 (mtt) REVERT: E 131 ARG cc_start: 0.9063 (mtm180) cc_final: 0.8850 (mtm180) REVERT: H 101 LEU cc_start: 0.8894 (mm) cc_final: 0.8682 (mm) outliers start: 7 outliers final: 5 residues processed: 92 average time/residue: 0.3599 time to fit residues: 45.3171 Evaluate side-chains 95 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 73 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 0.0570 chunk 105 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 83 HIS L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14854 Z= 0.188 Angle : 0.531 8.155 21338 Z= 0.316 Chirality : 0.035 0.134 2417 Planarity : 0.004 0.046 1686 Dihedral : 29.401 176.442 4329 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.94 % Allowed : 11.84 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.65 (0.27), residues: 982 helix: 2.13 (0.21), residues: 632 sheet: 0.46 (0.96), residues: 24 loop : -0.99 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 61 HIS 0.008 0.001 HIS H 49 PHE 0.009 0.001 PHE B 61 TYR 0.024 0.001 TYR L 134 ARG 0.003 0.000 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9511 (p) cc_final: 0.9301 (p) REVERT: E 131 ARG cc_start: 0.9060 (mtm180) cc_final: 0.8844 (mtm180) REVERT: L 38 MET cc_start: 0.7004 (tpp) cc_final: 0.6718 (mmm) outliers start: 8 outliers final: 5 residues processed: 96 average time/residue: 0.3498 time to fit residues: 46.0487 Evaluate side-chains 94 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 73 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14854 Z= 0.214 Angle : 0.542 7.925 21338 Z= 0.320 Chirality : 0.036 0.139 2417 Planarity : 0.004 0.047 1686 Dihedral : 29.446 176.557 4329 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.52 % Allowed : 12.08 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.64 (0.27), residues: 982 helix: 2.11 (0.21), residues: 634 sheet: 0.59 (0.98), residues: 24 loop : -0.99 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 61 HIS 0.003 0.001 HIS A 113 PHE 0.009 0.001 PHE B 61 TYR 0.025 0.001 TYR L 134 ARG 0.003 0.000 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9535 (p) cc_final: 0.9333 (p) REVERT: E 131 ARG cc_start: 0.9082 (mtm180) cc_final: 0.8876 (mtm180) REVERT: G 78 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8194 (mp) REVERT: H 99 ARG cc_start: 0.8328 (mtt180) cc_final: 0.8100 (ttm-80) outliers start: 13 outliers final: 7 residues processed: 103 average time/residue: 0.3614 time to fit residues: 50.5637 Evaluate side-chains 101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 73 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14854 Z= 0.182 Angle : 0.538 8.646 21338 Z= 0.318 Chirality : 0.035 0.174 2417 Planarity : 0.004 0.048 1686 Dihedral : 29.432 176.429 4329 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.17 % Allowed : 12.78 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.73 (0.27), residues: 982 helix: 2.20 (0.21), residues: 633 sheet: 0.34 (0.99), residues: 24 loop : -0.96 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 61 HIS 0.003 0.001 HIS C 31 PHE 0.008 0.001 PHE B 61 TYR 0.024 0.001 TYR L 134 ARG 0.004 0.000 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9533 (p) cc_final: 0.9331 (p) REVERT: G 78 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8187 (mp) REVERT: H 99 ARG cc_start: 0.8334 (mtt180) cc_final: 0.8099 (ttm-80) REVERT: L 38 MET cc_start: 0.6967 (tpp) cc_final: 0.6734 (mmm) outliers start: 10 outliers final: 8 residues processed: 96 average time/residue: 0.3636 time to fit residues: 47.7271 Evaluate side-chains 98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 73 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14854 Z= 0.193 Angle : 0.535 8.059 21338 Z= 0.317 Chirality : 0.035 0.136 2417 Planarity : 0.004 0.045 1686 Dihedral : 29.417 176.759 4329 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.17 % Allowed : 13.01 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.74 (0.27), residues: 982 helix: 2.20 (0.21), residues: 633 sheet: 0.30 (0.98), residues: 24 loop : -0.94 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 61 HIS 0.002 0.001 HIS C 31 PHE 0.008 0.001 PHE B 61 TYR 0.023 0.001 TYR L 134 ARG 0.006 0.000 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9525 (p) cc_final: 0.9310 (p) REVERT: G 78 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8185 (mp) REVERT: H 99 ARG cc_start: 0.8339 (mtt180) cc_final: 0.8104 (ttm-80) REVERT: L 38 MET cc_start: 0.6989 (tpp) cc_final: 0.6784 (mmm) outliers start: 10 outliers final: 8 residues processed: 96 average time/residue: 0.3543 time to fit residues: 46.9119 Evaluate side-chains 101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 73 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14854 Z= 0.256 Angle : 0.560 8.414 21338 Z= 0.328 Chirality : 0.037 0.136 2417 Planarity : 0.004 0.046 1686 Dihedral : 29.526 176.573 4329 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.41 % Allowed : 12.54 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.56 (0.27), residues: 982 helix: 2.06 (0.21), residues: 635 sheet: 0.12 (1.00), residues: 24 loop : -1.02 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 61 HIS 0.004 0.001 HIS A 113 PHE 0.010 0.001 PHE A 78 TYR 0.023 0.001 TYR L 134 ARG 0.006 0.000 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9539 (p) cc_final: 0.9317 (p) REVERT: E 59 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8077 (pm20) REVERT: G 78 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8202 (mp) REVERT: G 92 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: H 99 ARG cc_start: 0.8323 (mtt180) cc_final: 0.8113 (ttm-80) REVERT: L 1 MET cc_start: 0.6343 (ppp) cc_final: 0.5636 (mtm) REVERT: L 38 MET cc_start: 0.6995 (tpp) cc_final: 0.6789 (mmm) outliers start: 12 outliers final: 8 residues processed: 97 average time/residue: 0.3637 time to fit residues: 48.7688 Evaluate side-chains 98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 73 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 10 optimal weight: 0.0470 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14854 Z= 0.164 Angle : 0.544 8.012 21338 Z= 0.323 Chirality : 0.035 0.172 2417 Planarity : 0.005 0.056 1686 Dihedral : 29.471 176.111 4329 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.06 % Allowed : 13.36 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.78 (0.27), residues: 982 helix: 2.25 (0.21), residues: 634 sheet: 0.05 (1.02), residues: 24 loop : -0.95 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 61 HIS 0.003 0.001 HIS C 31 PHE 0.007 0.001 PHE B 61 TYR 0.021 0.001 TYR L 134 ARG 0.006 0.000 ARG K 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9528 (p) cc_final: 0.9310 (p) REVERT: G 78 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8187 (mp) REVERT: G 92 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: H 99 ARG cc_start: 0.8324 (mtt180) cc_final: 0.8103 (ttm-80) REVERT: L 1 MET cc_start: 0.6319 (ppp) cc_final: 0.5451 (ttt) outliers start: 9 outliers final: 7 residues processed: 99 average time/residue: 0.3400 time to fit residues: 46.4622 Evaluate side-chains 107 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 73 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.151710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.112314 restraints weight = 16536.481| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.03 r_work: 0.2784 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14854 Z= 0.264 Angle : 0.571 10.194 21338 Z= 0.332 Chirality : 0.037 0.185 2417 Planarity : 0.005 0.051 1686 Dihedral : 29.529 176.421 4329 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.29 % Allowed : 13.01 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.55 (0.27), residues: 982 helix: 2.07 (0.21), residues: 635 sheet: -0.01 (1.01), residues: 24 loop : -1.05 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 61 HIS 0.004 0.001 HIS A 113 PHE 0.010 0.001 PHE A 78 TYR 0.021 0.001 TYR L 134 ARG 0.004 0.000 ARG K 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2319.55 seconds wall clock time: 43 minutes 11.49 seconds (2591.49 seconds total)