Starting phenix.real_space_refine on Tue Nov 19 03:46:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn1_40609/11_2024/8sn1_40609.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn1_40609/11_2024/8sn1_40609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn1_40609/11_2024/8sn1_40609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn1_40609/11_2024/8sn1_40609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn1_40609/11_2024/8sn1_40609.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn1_40609/11_2024/8sn1_40609.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. 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 7891 2.51 5 N 2608 2.21 5 O 3171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13998 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: 691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Conformer: "B" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} bond proxies already assigned to first conformer: 698 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 34.621 67.720 41.713 1.00 71.54 S ATOM 12446 SG CYS K 51 32.912 64.309 42.021 1.00 58.73 S ATOM 12470 SG CYS K 54 34.765 65.302 38.806 1.00 65.25 S ATOM 12187 SG CYS K 16 21.868 63.309 48.158 1.00 77.69 S ATOM 12205 SG CYS K 19 21.177 60.743 51.004 1.00 79.04 S ATOM 12335 SG CYS K 36 23.454 63.950 51.370 1.00 71.93 S ATOM 12357 SG CYS K 39 24.693 61.015 49.965 1.00 70.40 S Time building chain proxies: 7.76, per 1000 atoms: 0.55 Number of scatterers: 13998 At special positions: 0 Unit cell: (110.224, 130.144, 124.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 32 16.00 P 294 15.00 O 3171 8.00 N 2608 7.00 C 7891 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: 3.64 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 9 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 11 sheets defined 64.3% alpha, 4.4% beta 135 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 5.63 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.564A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.585A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.924A 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: 3.877A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.591A 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: 3.659A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.693A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.558A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.782A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.535A pdb=" N SER D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.822A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.624A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.678A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.782A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.744A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.898A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.573A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.522A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.642A pdb=" N MET H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.613A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.764A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 removed outlier: 3.674A pdb=" N GLU K 45 " --> pdb=" O GLN K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.766A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 removed outlier: 3.772A pdb=" N ILE K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS K 83 " --> pdb=" O ILE K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 91 removed outlier: 4.374A 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: 3.718A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 Processing helix chain 'L' and resid 131 through 143 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.200A 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: 7.435A 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 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.252A 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 77 through 78 removed outlier: 3.550A pdb=" N ILE G 78 " --> pdb=" O GLY H 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24 458 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 4.06 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: 2909 1.33 - 1.45: 4520 1.45 - 1.57: 6802 1.57 - 1.69: 586 1.69 - 1.81: 47 Bond restraints: 14864 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 1.67e+00 bond pdb=" CG1 ILE L 54 " pdb=" CD1 ILE L 54 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.34e+00 bond pdb=" CG1 ILE H 54 " pdb=" CD1 ILE H 54 " ideal model delta sigma weight residual 1.513 1.558 -0.045 3.90e-02 6.57e+02 1.33e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 9.58e-01 ... (remaining 14859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 20384 1.13 - 2.26: 820 2.26 - 3.39: 127 3.39 - 4.51: 8 4.51 - 5.64: 14 Bond angle restraints: 21353 Sorted by residual: angle pdb=" C ALA L 19 " pdb=" N GLN L 20 " pdb=" CA GLN L 20 " ideal model delta sigma weight residual 121.54 126.24 -4.70 1.91e+00 2.74e-01 6.06e+00 angle pdb=" CA GLN L 20 " pdb=" CB GLN L 20 " pdb=" CG GLN L 20 " ideal model delta sigma weight residual 114.10 118.63 -4.53 2.00e+00 2.50e-01 5.13e+00 angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 122.46 125.47 -3.01 1.41e+00 5.03e-01 4.56e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 118.22 -5.04 2.37e+00 1.78e-01 4.53e+00 angle pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 102.40 105.43 -3.03 1.50e+00 4.44e-01 4.08e+00 ... (remaining 21348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 6796 35.27 - 70.54: 1405 70.54 - 105.81: 21 105.81 - 141.08: 0 141.08 - 176.35: 2 Dihedral angle restraints: 8224 sinusoidal: 5302 harmonic: 2922 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 70.74 149.26 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CB GLU G 91 " pdb=" CG GLU G 91 " pdb=" CD GLU G 91 " pdb=" OE1 GLU G 91 " ideal model delta sinusoidal sigma weight residual 0.00 89.86 -89.86 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 8221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1764 0.034 - 0.067: 515 0.067 - 0.101: 101 0.101 - 0.134: 36 0.134 - 0.168: 3 Chirality restraints: 2419 Sorted by residual: chirality pdb=" CA ILE L 54 " pdb=" N ILE L 54 " pdb=" C ILE L 54 " pdb=" CB ILE L 54 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CA VAL L 67 " pdb=" N VAL L 67 " pdb=" C VAL L 67 " pdb=" CB VAL L 67 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ILE H 54 " pdb=" N ILE H 54 " pdb=" C ILE H 54 " pdb=" CB ILE H 54 " 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 2416 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 60 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO L 61 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.025 2.00e-02 2.50e+03 1.09e-02 3.24e+00 pdb=" N9 DA I -35 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO D 103 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.024 5.00e-02 4.00e+02 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1790 2.76 - 3.47: 17738 3.47 - 4.19: 37384 4.19 - 4.90: 58549 Nonbonded interactions: 115463 Sorted by model distance: nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.329 3.350 nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.330 3.350 nonbonded pdb=" N SER C 11 " pdb=" O SER D 123 " model vdw 2.246 3.120 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.247 3.040 nonbonded pdb=" N SER G 11 " pdb=" O SER H 123 " model vdw 2.252 3.120 ... (remaining 115458 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=0.17 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 36.940 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 41.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 0.045 14864 Z= 0.167 Angle : 0.523 5.642 21353 Z= 0.311 Chirality : 0.034 0.168 2419 Planarity : 0.004 0.047 1688 Dihedral : 26.479 176.350 6336 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.12 % Allowed : 0.23 % Favored : 99.65 % 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: 1.60 (0.27), residues: 983 helix: 2.10 (0.21), residues: 628 sheet: -0.62 (1.11), residues: 24 loop : -0.89 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 61 HIS 0.004 0.001 HIS C 82 PHE 0.010 0.001 PHE L 69 TYR 0.020 0.001 TYR C 50 ARG 0.003 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 99 ARG cc_start: 0.7946 (mtt-85) cc_final: 0.7258 (mtm180) REVERT: E 122 LYS cc_start: 0.8891 (pttt) cc_final: 0.8580 (ptmt) REVERT: E 129 ARG cc_start: 0.8628 (tmt170) cc_final: 0.8415 (tpt90) REVERT: H 33 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7404 (mtt180) REVERT: H 79 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.8038 (mtm180) REVERT: L 147 MET cc_start: 0.3445 (pmm) cc_final: 0.2318 (mtt) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3638 time to fit residues: 51.3941 Evaluate side-chains 87 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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: 6.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN K 65 HIS L 46 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14864 Z= 0.245 Angle : 0.552 5.639 21353 Z= 0.325 Chirality : 0.036 0.153 2419 Planarity : 0.004 0.044 1688 Dihedral : 29.617 175.686 4332 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.58 % Allowed : 5.14 % Favored : 94.28 % 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: 1.54 (0.27), residues: 983 helix: 2.07 (0.21), residues: 638 sheet: -0.72 (1.11), residues: 24 loop : -1.02 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 61 HIS 0.003 0.001 HIS A 39 PHE 0.009 0.001 PHE F 61 TYR 0.011 0.001 TYR H 121 ARG 0.003 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8886 (mttm) cc_final: 0.8442 (mtpp) REVERT: D 47 GLN cc_start: 0.8749 (mt0) cc_final: 0.8535 (mt0) REVERT: D 99 ARG cc_start: 0.7937 (mtt-85) cc_final: 0.7403 (mtm180) REVERT: E 122 LYS cc_start: 0.8887 (pttt) cc_final: 0.8611 (ptmt) REVERT: E 129 ARG cc_start: 0.8691 (tmt170) cc_final: 0.8329 (tpt90) REVERT: G 73 ASN cc_start: 0.7902 (t0) cc_final: 0.7506 (t0) REVERT: L 4 LYS cc_start: 0.8110 (mttt) cc_final: 0.7885 (mttp) REVERT: L 92 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7931 (mm-40) REVERT: L 147 MET cc_start: 0.3506 (pmm) cc_final: 0.2257 (mtt) outliers start: 4 outliers final: 3 residues processed: 94 average time/residue: 0.3571 time to fit residues: 45.2725 Evaluate side-chains 91 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain L residue 94 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14864 Z= 0.349 Angle : 0.601 6.402 21353 Z= 0.349 Chirality : 0.039 0.147 2419 Planarity : 0.005 0.045 1688 Dihedral : 30.024 173.965 4332 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.93 % Allowed : 8.53 % Favored : 90.54 % 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: 1.19 (0.27), residues: 983 helix: 1.80 (0.21), residues: 637 sheet: -0.71 (1.12), residues: 24 loop : -1.20 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 61 HIS 0.006 0.001 HIS E 113 PHE 0.012 0.002 PHE F 61 TYR 0.014 0.002 TYR H 121 ARG 0.006 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 1.207 Fit side-chains REVERT: C 36 LYS cc_start: 0.8882 (mttm) cc_final: 0.8446 (mtpp) REVERT: D 47 GLN cc_start: 0.8770 (mt0) cc_final: 0.8540 (mt0) REVERT: D 99 ARG cc_start: 0.7962 (mtt-85) cc_final: 0.7239 (mtm180) REVERT: E 129 ARG cc_start: 0.8606 (tmt170) cc_final: 0.8233 (tpt90) REVERT: G 19 SER cc_start: 0.8820 (m) cc_final: 0.8595 (m) REVERT: G 73 ASN cc_start: 0.7787 (t0) cc_final: 0.7383 (t0) REVERT: K 50 CYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8042 (m) REVERT: L 147 MET cc_start: 0.3486 (pmm) cc_final: 0.2172 (mtt) outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 0.3486 time to fit residues: 43.4579 Evaluate side-chains 87 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 50 CYS Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 94 SER 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: 0.7980 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8158 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14864 Z= 0.195 Angle : 0.537 5.324 21353 Z= 0.318 Chirality : 0.035 0.136 2419 Planarity : 0.004 0.043 1688 Dihedral : 29.762 174.771 4332 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.58 % Allowed : 9.81 % Favored : 89.60 % 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: 1.49 (0.27), residues: 983 helix: 2.04 (0.21), residues: 640 sheet: -0.76 (1.11), residues: 24 loop : -1.10 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 61 HIS 0.003 0.001 HIS A 39 PHE 0.008 0.001 PHE L 62 TYR 0.009 0.001 TYR F 51 ARG 0.004 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: D 47 GLN cc_start: 0.8755 (mt0) cc_final: 0.8545 (mt0) REVERT: D 99 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7394 (mtm180) REVERT: E 129 ARG cc_start: 0.8613 (tmt170) cc_final: 0.8332 (tpt90) REVERT: G 19 SER cc_start: 0.8754 (m) cc_final: 0.8541 (m) REVERT: G 73 ASN cc_start: 0.7893 (t0) cc_final: 0.7427 (t0) REVERT: H 59 MET cc_start: 0.8669 (tpp) cc_final: 0.8082 (mmm) REVERT: L 92 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7872 (mm-40) REVERT: L 147 MET cc_start: 0.3463 (pmm) cc_final: 0.2184 (mtt) outliers start: 4 outliers final: 3 residues processed: 89 average time/residue: 0.3969 time to fit residues: 47.5911 Evaluate side-chains 89 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 94 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 29 optimal weight: 0.0770 chunk 39 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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: 0.8109 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14864 Z= 0.173 Angle : 0.507 5.247 21353 Z= 0.303 Chirality : 0.034 0.133 2419 Planarity : 0.004 0.041 1688 Dihedral : 29.419 175.297 4332 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.93 % Allowed : 10.40 % Favored : 88.67 % 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: 1.79 (0.27), residues: 983 helix: 2.31 (0.21), residues: 638 sheet: -0.71 (1.12), residues: 24 loop : -1.04 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 61 HIS 0.003 0.001 HIS A 39 PHE 0.008 0.001 PHE A 67 TYR 0.007 0.001 TYR F 51 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 1.096 Fit side-chains REVERT: C 36 LYS cc_start: 0.8869 (mttm) cc_final: 0.8453 (mtpp) REVERT: C 92 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: D 47 GLN cc_start: 0.8762 (mt0) cc_final: 0.8528 (mt0) REVERT: D 99 ARG cc_start: 0.7948 (mtt-85) cc_final: 0.7406 (mtm180) REVERT: E 122 LYS cc_start: 0.8970 (pttt) cc_final: 0.8635 (ptmt) REVERT: E 129 ARG cc_start: 0.8663 (tmt170) cc_final: 0.8412 (tpt90) REVERT: G 19 SER cc_start: 0.8720 (m) cc_final: 0.8510 (m) REVERT: G 73 ASN cc_start: 0.7867 (t0) cc_final: 0.7411 (t0) REVERT: H 59 MET cc_start: 0.8567 (tpp) cc_final: 0.8041 (mmm) REVERT: L 38 MET cc_start: 0.5518 (mmm) cc_final: 0.5308 (mtm) REVERT: L 147 MET cc_start: 0.3334 (pmm) cc_final: 0.2115 (mtt) outliers start: 7 outliers final: 4 residues processed: 94 average time/residue: 0.3671 time to fit residues: 46.8538 Evaluate side-chains 97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain L residue 94 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 10.0000 chunk 23 optimal weight: 0.0030 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.0370 chunk 61 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 overall best weight: 0.3068 ------------------------------------------------------------------------------- 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: 0.8090 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14864 Z= 0.147 Angle : 0.506 5.271 21353 Z= 0.302 Chirality : 0.034 0.135 2419 Planarity : 0.004 0.040 1688 Dihedral : 29.375 175.520 4332 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.93 % Allowed : 11.45 % Favored : 87.62 % 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: 1.95 (0.27), residues: 983 helix: 2.43 (0.21), residues: 638 sheet: -0.72 (1.12), residues: 24 loop : -0.97 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 61 HIS 0.003 0.001 HIS A 39 PHE 0.008 0.001 PHE L 62 TYR 0.006 0.001 TYR F 51 ARG 0.004 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 1.067 Fit side-chains REVERT: C 36 LYS cc_start: 0.8930 (mttm) cc_final: 0.8501 (mtpp) REVERT: D 47 GLN cc_start: 0.8751 (mt0) cc_final: 0.8519 (mt0) REVERT: D 99 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7388 (mtm180) REVERT: E 122 LYS cc_start: 0.8912 (pttt) cc_final: 0.8611 (ptmt) REVERT: E 129 ARG cc_start: 0.8642 (tmt170) cc_final: 0.8396 (tpt90) REVERT: G 19 SER cc_start: 0.8705 (m) cc_final: 0.8495 (m) REVERT: G 73 ASN cc_start: 0.7829 (t0) cc_final: 0.7392 (t0) REVERT: H 59 MET cc_start: 0.8529 (tpp) cc_final: 0.8019 (mmm) REVERT: L 147 MET cc_start: 0.3306 (pmm) cc_final: 0.2100 (mtt) outliers start: 7 outliers final: 4 residues processed: 97 average time/residue: 0.3702 time to fit residues: 48.9143 Evaluate side-chains 96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain L residue 94 SER 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: 0.0470 chunk 86 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 0.0870 chunk 73 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14864 Z= 0.156 Angle : 0.503 5.435 21353 Z= 0.300 Chirality : 0.033 0.165 2419 Planarity : 0.004 0.038 1688 Dihedral : 29.299 176.337 4332 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.40 % Allowed : 11.57 % Favored : 87.03 % 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: 2.03 (0.27), residues: 983 helix: 2.52 (0.21), residues: 638 sheet: -0.83 (1.12), residues: 24 loop : -0.97 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 61 HIS 0.003 0.001 HIS A 39 PHE 0.008 0.001 PHE L 62 TYR 0.008 0.001 TYR F 51 ARG 0.002 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.074 Fit side-chains REVERT: A 109 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8023 (mp) REVERT: C 36 LYS cc_start: 0.8869 (mttm) cc_final: 0.8470 (mtpp) REVERT: C 92 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: D 47 GLN cc_start: 0.8754 (mt0) cc_final: 0.8530 (mt0) REVERT: D 99 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7448 (mtm180) REVERT: E 122 LYS cc_start: 0.8913 (pttt) cc_final: 0.8592 (pttt) REVERT: E 129 ARG cc_start: 0.8667 (tmt170) cc_final: 0.8418 (tpt90) REVERT: G 73 ASN cc_start: 0.7806 (t0) cc_final: 0.7364 (t0) REVERT: H 59 MET cc_start: 0.8503 (tpp) cc_final: 0.8001 (mmm) REVERT: L 52 LEU cc_start: 0.4988 (OUTLIER) cc_final: 0.4317 (pp) REVERT: L 147 MET cc_start: 0.3252 (pmm) cc_final: 0.2034 (mtt) outliers start: 11 outliers final: 7 residues processed: 101 average time/residue: 0.3466 time to fit residues: 47.4633 Evaluate side-chains 102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 22 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14864 Z= 0.176 Angle : 0.506 5.475 21353 Z= 0.302 Chirality : 0.034 0.161 2419 Planarity : 0.004 0.039 1688 Dihedral : 29.336 176.917 4332 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.40 % Allowed : 11.92 % Favored : 86.68 % 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: 1.97 (0.27), residues: 983 helix: 2.46 (0.21), residues: 638 sheet: -0.42 (1.19), residues: 24 loop : -1.02 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 61 HIS 0.003 0.001 HIS E 113 PHE 0.009 0.001 PHE L 56 TYR 0.006 0.001 TYR F 51 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.070 Fit side-chains REVERT: A 109 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8089 (mp) REVERT: C 36 LYS cc_start: 0.8930 (mttm) cc_final: 0.8508 (mtpp) REVERT: C 92 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: D 47 GLN cc_start: 0.8769 (mt0) cc_final: 0.8543 (mt0) REVERT: D 99 ARG cc_start: 0.7951 (mtt-85) cc_final: 0.7410 (mtm180) REVERT: E 122 LYS cc_start: 0.8913 (pttt) cc_final: 0.8609 (ptmt) REVERT: E 129 ARG cc_start: 0.8697 (tmt170) cc_final: 0.8434 (tpt90) REVERT: G 73 ASN cc_start: 0.7716 (t0) cc_final: 0.7294 (t0) REVERT: H 59 MET cc_start: 0.8559 (tpp) cc_final: 0.8029 (mmm) REVERT: L 52 LEU cc_start: 0.4834 (OUTLIER) cc_final: 0.4062 (pp) REVERT: L 147 MET cc_start: 0.3225 (pmm) cc_final: 0.2030 (mtt) outliers start: 11 outliers final: 8 residues processed: 100 average time/residue: 0.3659 time to fit residues: 50.3855 Evaluate side-chains 102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 94 SER 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: 0.9980 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: