Starting phenix.real_space_refine on Wed Apr 10 14:59:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn1_40609/04_2024/8sn1_40609.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn1_40609/04_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_40609/04_2024/8sn1_40609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn1_40609/04_2024/8sn1_40609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn1_40609/04_2024/8sn1_40609.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn1_40609/04_2024/8sn1_40609.pdb" } 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 Residue "A GLU 133": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 8.05, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.48 Conformation dependent library (CDL) restraints added in 2.4 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 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: 6.73 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: 5.09 Time building geometry restraints manager: 6.98 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: 98.83 - 105.87: 1710 105.87 - 112.92: 8124 112.92 - 119.96: 5355 119.96 - 127.00: 5433 127.00 - 134.05: 731 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 2.520 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.247 2.440 nonbonded pdb=" N SER G 11 " pdb=" O SER H 123 " model vdw 2.252 2.520 ... (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 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 4.380 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 47.640 Find NCS groups from input model: 0.560 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.840 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.972 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: 0.2957 time to fit residues: 41.6296 Evaluate side-chains 87 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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: 10.0000 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14864 Z= 0.281 Angle : 0.565 5.937 21353 Z= 0.331 Chirality : 0.037 0.156 2419 Planarity : 0.004 0.046 1688 Dihedral : 29.729 175.207 4332 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.70 % Allowed : 5.02 % 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: 1.48 (0.27), residues: 983 helix: 2.02 (0.21), residues: 633 sheet: -0.68 (1.11), residues: 24 loop : -1.00 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 61 HIS 0.004 0.001 HIS E 113 PHE 0.010 0.002 PHE F 61 TYR 0.012 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 93 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8906 (mttm) cc_final: 0.8470 (mtpp) REVERT: D 47 GLN cc_start: 0.8750 (mt0) cc_final: 0.8530 (mt0) REVERT: D 99 ARG cc_start: 0.7968 (mtt-85) cc_final: 0.7263 (mtm180) REVERT: E 129 ARG cc_start: 0.8642 (tmt170) cc_final: 0.8370 (tpt90) REVERT: G 73 ASN cc_start: 0.7812 (t0) cc_final: 0.7467 (t0) REVERT: L 4 LYS cc_start: 0.8103 (mttt) cc_final: 0.7886 (mttp) REVERT: L 147 MET cc_start: 0.3576 (pmm) cc_final: 0.2260 (mtt) outliers start: 5 outliers final: 4 residues processed: 90 average time/residue: 0.3723 time to fit residues: 45.1071 Evaluate side-chains 91 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR 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: 0.8980 chunk 110 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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: 0.8198 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14864 Z= 0.310 Angle : 0.578 6.084 21353 Z= 0.338 Chirality : 0.038 0.148 2419 Planarity : 0.005 0.045 1688 Dihedral : 29.934 173.704 4332 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.70 % Allowed : 8.41 % Favored : 90.89 % 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: 1.25 (0.27), residues: 983 helix: 1.85 (0.21), residues: 638 sheet: -0.59 (1.14), residues: 24 loop : -1.19 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 61 HIS 0.004 0.001 HIS E 113 PHE 0.011 0.002 PHE F 61 TYR 0.011 0.001 TYR H 121 ARG 0.005 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 94 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 1.083 Fit side-chains REVERT: C 36 LYS cc_start: 0.8884 (mttm) cc_final: 0.8446 (mtpp) REVERT: D 47 GLN cc_start: 0.8780 (mt0) cc_final: 0.8562 (mt0) REVERT: D 99 ARG cc_start: 0.7958 (mtt-85) cc_final: 0.7233 (mtm180) REVERT: E 129 ARG cc_start: 0.8765 (tmt170) cc_final: 0.8480 (tpt90) REVERT: G 73 ASN cc_start: 0.7790 (t0) cc_final: 0.7381 (t0) REVERT: L 147 MET cc_start: 0.3515 (pmm) cc_final: 0.2232 (mtt) outliers start: 5 outliers final: 4 residues processed: 92 average time/residue: 0.3568 time to fit residues: 44.4678 Evaluate side-chains 90 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 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: 0.8154 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14864 Z= 0.189 Angle : 0.534 5.363 21353 Z= 0.317 Chirality : 0.036 0.137 2419 Planarity : 0.004 0.043 1688 Dihedral : 29.747 174.441 4332 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.82 % Allowed : 10.16 % Favored : 89.02 % 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: 2.08 (0.21), residues: 639 sheet: -0.69 (1.11), residues: 24 loop : -1.08 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 61 HIS 0.004 0.001 HIS A 39 PHE 0.007 0.001 PHE L 62 TYR 0.008 0.001 TYR F 51 ARG 0.003 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 92 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 1.429 Fit side-chains REVERT: C 36 LYS cc_start: 0.8881 (mttm) cc_final: 0.8471 (mtpp) REVERT: D 47 GLN cc_start: 0.8755 (mt0) cc_final: 0.8539 (mt0) REVERT: D 99 ARG cc_start: 0.7921 (mtt-85) cc_final: 0.7394 (mtm180) REVERT: E 129 ARG cc_start: 0.8704 (tmt170) cc_final: 0.8404 (tpt90) REVERT: G 73 ASN cc_start: 0.7847 (t0) cc_final: 0.7392 (t0) REVERT: H 59 MET cc_start: 0.8647 (tpp) cc_final: 0.8071 (mmm) REVERT: L 4 LYS cc_start: 0.8212 (mttp) cc_final: 0.7860 (mptt) REVERT: L 147 MET cc_start: 0.3414 (pmm) cc_final: 0.2171 (mtt) outliers start: 6 outliers final: 5 residues processed: 89 average time/residue: 0.3588 time to fit residues: 43.0920 Evaluate side-chains 94 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain C residue 76 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 100 optimal weight: 0.0670 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 29 optimal weight: 0.0670 chunk 39 optimal weight: 0.9980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1201 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= 0.161 Angle : 0.496 5.193 21353 Z= 0.297 Chirality : 0.033 0.146 2419 Planarity : 0.004 0.040 1688 Dihedral : 29.197 176.201 4332 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.82 % Allowed : 11.21 % Favored : 87.97 % 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: 1.93 (0.27), residues: 983 helix: 2.44 (0.21), residues: 638 sheet: -0.79 (1.08), residues: 24 loop : -1.02 (0.31), 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 0.007 0.001 PHE A 67 TYR 0.006 0.001 TYR F 51 ARG 0.005 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 101 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 1.210 Fit side-chains REVERT: C 36 LYS cc_start: 0.8872 (mttm) cc_final: 0.8474 (mtpp) REVERT: C 92 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: D 47 GLN cc_start: 0.8766 (mt0) cc_final: 0.8538 (mt0) REVERT: D 99 ARG cc_start: 0.7947 (mtt-85) cc_final: 0.7414 (mtm180) REVERT: E 122 LYS cc_start: 0.8960 (pttt) cc_final: 0.8625 (ptmt) REVERT: E 129 ARG cc_start: 0.8626 (tmt170) cc_final: 0.8400 (tpt90) REVERT: G 73 ASN cc_start: 0.7642 (t0) cc_final: 0.7227 (t0) REVERT: L 4 LYS cc_start: 0.7954 (mttp) cc_final: 0.7724 (mttp) REVERT: L 38 MET cc_start: 0.5557 (mmm) cc_final: 0.5340 (mtm) REVERT: L 147 MET cc_start: 0.3396 (pmm) cc_final: 0.2211 (mtt) outliers start: 6 outliers final: 3 residues processed: 98 average time/residue: 0.3763 time to fit residues: 49.2199 Evaluate side-chains 98 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 90 THR 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: 0.9980 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.8098 moved from start: 0.1178 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= 0.182 Angle : 0.505 5.277 21353 Z= 0.301 Chirality : 0.034 0.147 2419 Planarity : 0.004 0.041 1688 Dihedral : 29.318 177.377 4332 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.05 % Allowed : 11.92 % 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: 1.92 (0.27), residues: 983 helix: 2.42 (0.21), residues: 639 sheet: -0.68 (1.11), residues: 24 loop : -1.02 (0.31), residues: 320 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 0.007 0.001 PHE L 62 TYR 0.007 0.001 TYR F 51 ARG 0.003 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 102 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.120 Fit side-chains REVERT: C 36 LYS cc_start: 0.8860 (mttm) cc_final: 0.8462 (mtpp) REVERT: C 92 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: D 47 GLN cc_start: 0.8754 (mt0) cc_final: 0.8506 (mt0) REVERT: D 99 ARG cc_start: 0.7953 (mtt-85) cc_final: 0.7425 (mtm180) REVERT: E 122 LYS cc_start: 0.8886 (pttt) cc_final: 0.8580 (ptmt) REVERT: E 129 ARG cc_start: 0.8683 (tmt170) cc_final: 0.8474 (tpt90) REVERT: G 73 ASN cc_start: 0.7740 (t0) cc_final: 0.7295 (t0) REVERT: L 4 LYS cc_start: 0.7988 (mttp) cc_final: 0.7743 (mttp) REVERT: L 38 MET cc_start: 0.5325 (mmm) cc_final: 0.5064 (mtm) REVERT: L 147 MET cc_start: 0.3321 (pmm) cc_final: 0.2177 (mtt) outliers start: 8 outliers final: 6 residues processed: 99 average time/residue: 0.3580 time to fit residues: 47.8644 Evaluate side-chains 97 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 90 THR 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: 1.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.8180 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14864 Z= 0.281 Angle : 0.560 5.709 21353 Z= 0.328 Chirality : 0.037 0.156 2419 Planarity : 0.004 0.042 1688 Dihedral : 29.704 175.296 4332 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.17 % Allowed : 12.50 % Favored : 86.33 % 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: 1.53 (0.27), residues: 983 helix: 2.12 (0.21), residues: 638 sheet: -0.71 (1.11), residues: 24 loop : -1.18 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 61 HIS 0.005 0.001 HIS E 113 PHE 0.012 0.002 PHE F 61 TYR 0.011 0.001 TYR H 121 ARG 0.003 0.000 ARG E 116 *********************** 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 100 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: D 47 GLN cc_start: 0.8782 (mt0) cc_final: 0.8565 (mt0) REVERT: D 99 ARG cc_start: 0.7946 (mtt-85) cc_final: 0.7408 (mtm180) REVERT: E 129 ARG cc_start: 0.8693 (tmt170) cc_final: 0.8383 (tpt90) REVERT: G 73 ASN cc_start: 0.7757 (t0) cc_final: 0.7306 (t0) REVERT: L 4 LYS cc_start: 0.8046 (mttp) cc_final: 0.7749 (mttp) REVERT: L 52 LEU cc_start: 0.4820 (OUTLIER) cc_final: 0.4007 (pp) REVERT: L 147 MET cc_start: 0.3443 (pmm) cc_final: 0.2157 (mtt) outliers start: 9 outliers final: 6 residues processed: 98 average time/residue: 0.3698 time to fit residues: 48.6625 Evaluate side-chains 98 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 LYS 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: 0.7980 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 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: 0.8155 moved from start: 0.1139 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= 0.192 Angle : 0.536 5.913 21353 Z= 0.318 Chirality : 0.035 0.153 2419 Planarity : 0.004 0.052 1688 Dihedral : 29.623 175.008 4332 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.29 % Allowed : 12.50 % Favored : 86.21 % 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: 983 helix: 2.20 (0.21), residues: 639 sheet: -0.73 (1.10), residues: 24 loop : -1.15 (0.31), residues: 320 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 0.015 0.001 PHE L 56 TYR 0.007 0.001 TYR H 121 ARG 0.009 0.000 ARG C 35 *********************** 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 fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 109 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8144 (mp) REVERT: C 92 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: D 47 GLN cc_start: 0.8763 (mt0) cc_final: 0.8542 (mt0) REVERT: D 99 ARG cc_start: 0.7938 (mtt-85) cc_final: 0.7400 (mtm180) REVERT: E 129 ARG cc_start: 0.8730 (tmt170) cc_final: 0.8403 (tpt90) REVERT: G 73 ASN cc_start: 0.7721 (t0) cc_final: 0.7270 (t0) REVERT: L 4 LYS cc_start: 0.8045 (mttp) cc_final: 0.7743 (mttp) REVERT: L 52 LEU cc_start: 0.4920 (OUTLIER) cc_final: 0.4092 (pp) REVERT: L 147 MET cc_start: 0.3412 (pmm) cc_final: 0.2147 (mtt) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.3436 time to fit residues: 47.1970 Evaluate side-chains 103 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 LYS 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: 6.9990 chunk 102 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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: 0.8221 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 14864 Z= 0.368 Angle : 0.612 6.209 21353 Z= 0.355 Chirality : 0.040 0.157 2419 Planarity : 0.005 0.045 1688 Dihedral : 30.035 173.085 4332 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.40 % Allowed : 12.62 % Favored : 85.98 % 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: 1.17 (0.27), residues: 983 helix: 1.86 (0.21), residues: 638 sheet: -0.74 (1.10), residues: 24 loop : -1.38 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 141 HIS 0.008 0.001 HIS E 113 PHE 0.013 0.002 PHE F 61 TYR 0.014 0.002 TYR H 121 ARG 0.007 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 9 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 100 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.948 Fit side-chains REVERT: A 109 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8215 (mp) REVERT: C 36 LYS cc_start: 0.8870 (mttm) cc_final: 0.8436 (mtpp) REVERT: C 92 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: D 47 GLN cc_start: 0.8889 (mt0) cc_final: 0.8659 (mt0) REVERT: D 99 ARG cc_start: 0.7971 (mtt-85) cc_final: 0.7440 (mtm180) REVERT: E 129 ARG cc_start: 0.8698 (tmt170) cc_final: 0.8364 (tpt90) REVERT: G 73 ASN cc_start: 0.7785 (t0) cc_final: 0.7327 (t0) REVERT: L 38 MET cc_start: 0.5602 (mmm) cc_final: 0.5399 (mtm) REVERT: L 52 LEU cc_start: 0.4675 (OUTLIER) cc_final: 0.3783 (pp) REVERT: L 147 MET cc_start: 0.3552 (pmm) cc_final: 0.2202 (mtt) outliers start: 11 outliers final: 8 residues processed: 96 average time/residue: 0.3519 time to fit residues: 46.1565 Evaluate side-chains 100 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.0070 chunk 54 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- 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: 0.8203 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14864 Z= 0.283 Angle : 0.577 6.849 21353 Z= 0.339 Chirality : 0.038 0.155 2419 Planarity : 0.004 0.043 1688 Dihedral : 29.949 172.883 4332 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.29 % Allowed : 12.62 % Favored : 86.10 % 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: 1.20 (0.27), residues: 983 helix: 1.89 (0.21), residues: 639 sheet: -0.81 (1.09), residues: 24 loop : -1.37 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 61 HIS 0.006 0.001 HIS E 113 PHE 0.011 0.002 PHE L 56 TYR 0.010 0.001 TYR H 121 ARG 0.007 0.000 ARG C 35 ********************** REFINEMENT MACRO_CYCLE 10 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 99 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.150 Fit side-chains REVERT: A 109 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8195 (mp) REVERT: C 36 LYS cc_start: 0.8869 (mttm) cc_final: 0.8436 (mtpp) REVERT: C 92 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: D 47 GLN cc_start: 0.8884 (mt0) cc_final: 0.8652 (mt0) REVERT: D 99 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.7435 (mtm180) REVERT: E 129 ARG cc_start: 0.8684 (tmt170) cc_final: 0.8344 (tpt90) REVERT: G 73 ASN cc_start: 0.7764 (t0) cc_final: 0.7309 (t0) REVERT: L 38 MET cc_start: 0.5611 (mmm) cc_final: 0.5392 (mtm) REVERT: L 52 LEU cc_start: 0.4699 (OUTLIER) cc_final: 0.3835 (pp) REVERT: L 147 MET cc_start: 0.3528 (pmm) cc_final: 0.2199 (mtt) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.3597 time to fit residues: 46.8164 Evaluate side-chains 99 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.152055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.108204 restraints weight = 24452.277| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.19 r_work: 0.2579 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14864 Z= 0.290 Angle : 0.575 5.840 21353 Z= 0.336 Chirality : 0.037 0.153 2419 Planarity : 0.004 0.042 1688 Dihedral : 29.868 173.162 4332 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.40 % Allowed : 12.73 % Favored : 85.86 % 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: 1.23 (0.27), residues: 983 helix: 1.91 (0.21), residues: 638 sheet: -0.67 (1.12), residues: 24 loop : -1.39 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 61 HIS 0.006 0.001 HIS E 113 PHE 0.011 0.002 PHE F 61 TYR 0.012 0.001 TYR H 121 ARG 0.006 0.000 ARG C 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2339.60 seconds wall clock time: 49 minutes 54.88 seconds (2994.88 seconds total)