Starting phenix.real_space_refine on Mon Mar 18 03:44:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smy_40606/03_2024/8smy_40606.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smy_40606/03_2024/8smy_40606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smy_40606/03_2024/8smy_40606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smy_40606/03_2024/8smy_40606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smy_40606/03_2024/8smy_40606.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smy_40606/03_2024/8smy_40606.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.115 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 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 9": "OE1" <-> "OE2" Residue "L PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 87": "OD1" <-> "OD2" Residue "L ASP 112": "OD1" <-> "OD2" Residue "L ASP 117": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 32.961 68.212 47.437 1.00 46.50 S ATOM 12446 SG CYS K 51 31.741 64.804 46.427 1.00 38.48 S ATOM 12470 SG CYS K 54 31.689 67.804 43.930 1.00 45.98 S ATOM 12187 SG CYS K 16 23.164 61.088 52.931 1.00 62.13 S ATOM 12205 SG CYS K 19 21.277 58.686 55.106 1.00 60.25 S ATOM 12335 SG CYS K 36 24.123 60.787 56.601 1.00 49.24 S ATOM 12357 SG CYS K 39 25.001 57.974 54.445 1.00 47.55 S Time building chain proxies: 8.24, per 1000 atoms: 0.59 Number of scatterers: 13998 At special positions: 0 Unit cell: (108.896, 130.144, 127.488, 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: 6.30 Conformation dependent library (CDL) restraints added in 1.7 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 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " 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 63.4% alpha, 4.3% beta 137 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 5.84 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.697A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.706A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.642A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.836A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.608A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.724A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.737A 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: 3.541A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.564A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.661A 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: 4.180A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.618A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.881A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.595A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.757A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 90 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: 3.620A pdb=" N MET H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 58 through 67 removed outlier: 4.044A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 removed outlier: 3.656A pdb=" N ILE K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 91 removed outlier: 3.887A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 86 through 91 removed outlier: 3.703A 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 145 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.687A 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 removed outlier: 3.535A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.696A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.458A 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 101 through 102 removed outlier: 6.826A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.097A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.767A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 29 removed outlier: 3.788A pdb=" N HIS K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 25 452 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 698 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 4.84 Time building geometry restraints manager: 6.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3240 1.34 - 1.46: 4293 1.46 - 1.58: 6698 1.58 - 1.70: 586 1.70 - 1.82: 47 Bond restraints: 14864 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" CG ARG A 42 " pdb=" CD ARG A 42 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CA ASN L 79 " pdb=" C ASN L 79 " ideal model delta sigma weight residual 1.528 1.540 -0.012 1.33e-02 5.65e+03 8.57e-01 bond pdb=" CB PRO L 61 " pdb=" CG PRO L 61 " ideal model delta sigma weight residual 1.506 1.471 0.035 3.90e-02 6.57e+02 8.17e-01 ... (remaining 14859 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.77: 1635 105.77 - 112.86: 8190 112.86 - 119.96: 5382 119.96 - 127.06: 5453 127.06 - 134.15: 693 Bond angle restraints: 21353 Sorted by residual: angle pdb=" C TYR L 60 " pdb=" N PRO L 61 " pdb=" CD PRO L 61 " ideal model delta sigma weight residual 120.60 111.86 8.74 2.20e+00 2.07e-01 1.58e+01 angle pdb=" C SER L 80 " pdb=" N ASN L 81 " pdb=" CA ASN L 81 " ideal model delta sigma weight residual 121.94 116.43 5.51 2.00e+00 2.50e-01 7.60e+00 angle pdb=" N GLU L 140 " pdb=" CA GLU L 140 " pdb=" CB GLU L 140 " ideal model delta sigma weight residual 110.28 113.97 -3.69 1.55e+00 4.16e-01 5.68e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 118.29 -5.11 2.37e+00 1.78e-01 4.64e+00 angle pdb=" CA LEU K 49 " pdb=" CB LEU K 49 " pdb=" CG LEU K 49 " ideal model delta sigma weight residual 116.30 123.63 -7.33 3.50e+00 8.16e-02 4.39e+00 ... (remaining 21348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 6809 35.30 - 70.59: 1392 70.59 - 105.89: 21 105.89 - 141.19: 0 141.19 - 176.49: 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 43.51 176.49 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 66.28 153.72 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CB GLU G 41 " pdb=" CG GLU G 41 " pdb=" CD GLU G 41 " pdb=" OE1 GLU G 41 " ideal model delta sinusoidal sigma weight residual 0.00 89.70 -89.70 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 8221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1478 0.025 - 0.051: 607 0.051 - 0.076: 238 0.076 - 0.101: 60 0.101 - 0.126: 36 Chirality restraints: 2419 Sorted by residual: chirality pdb=" CA ILE G 79 " pdb=" N ILE G 79 " pdb=" C ILE G 79 " pdb=" CB ILE G 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE L 78 " pdb=" N ILE L 78 " pdb=" C ILE L 78 " pdb=" CB ILE L 78 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA ILE D 89 " pdb=" N ILE D 89 " pdb=" C ILE D 89 " pdb=" CB ILE D 89 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 2416 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 60 " -0.053 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO L 61 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 42 " -0.182 9.50e-02 1.11e+02 8.19e-02 4.21e+00 pdb=" NE ARG A 42 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 42 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 42 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 42 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS L 75 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO L 76 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO L 76 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 76 " -0.028 5.00e-02 4.00e+02 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1777 2.76 - 3.47: 17342 3.47 - 4.19: 37626 4.19 - 4.90: 58843 Nonbonded interactions: 115590 Sorted by model distance: nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.330 3.350 nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.332 3.350 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.162 2.520 nonbonded pdb=" OE2 GLU C 61 " pdb=" OG SER K 60 " model vdw 2.189 2.440 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.244 2.496 ... (remaining 115585 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: 0.010 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 4.880 Check model and map are aligned: 0.410 Set scattering table: 0.120 Process input model: 45.500 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14864 Z= 0.171 Angle : 0.536 8.742 21353 Z= 0.319 Chirality : 0.034 0.126 2419 Planarity : 0.005 0.082 1688 Dihedral : 26.398 176.486 6336 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 1.40 (0.27), residues: 983 helix: 1.87 (0.22), residues: 613 sheet: 0.67 (1.00), residues: 24 loop : -0.77 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 77 HIS 0.005 0.001 HIS L 75 PHE 0.009 0.001 PHE F 61 TYR 0.012 0.001 TYR L 134 ARG 0.009 0.000 ARG K 68 *********************** 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 117 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.124 Fit side-chains REVERT: A 58 THR cc_start: 0.9392 (p) cc_final: 0.9020 (p) REVERT: B 63 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7675 (mt-10) REVERT: G 74 LYS cc_start: 0.8650 (mttp) cc_final: 0.8190 (mmtm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3448 time to fit residues: 54.5491 Evaluate side-chains 104 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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: 1.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 0.0270 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN H 84 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.0522 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= 0.181 Angle : 0.523 6.456 21353 Z= 0.312 Chirality : 0.034 0.129 2419 Planarity : 0.004 0.051 1688 Dihedral : 29.140 176.714 4332 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.93 % Allowed : 5.49 % Favored : 93.57 % 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: 1.51 (0.27), residues: 983 helix: 1.90 (0.21), residues: 631 sheet: 0.74 (1.02), residues: 24 loop : -0.76 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 77 HIS 0.006 0.001 HIS L 75 PHE 0.008 0.001 PHE F 61 TYR 0.012 0.001 TYR D 121 ARG 0.006 0.000 ARG K 68 *********************** 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 116 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9381 (p) cc_final: 0.9012 (p) REVERT: B 63 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7689 (mt-10) REVERT: D 76 GLU cc_start: 0.8824 (tp30) cc_final: 0.8444 (tp30) REVERT: G 74 LYS cc_start: 0.8616 (mttp) cc_final: 0.8149 (mmtm) outliers start: 8 outliers final: 7 residues processed: 110 average time/residue: 0.3398 time to fit residues: 50.6518 Evaluate side-chains 111 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 119 optimal weight: 0.4980 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0747 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= 0.304 Angle : 0.572 8.120 21353 Z= 0.336 Chirality : 0.038 0.139 2419 Planarity : 0.005 0.049 1688 Dihedral : 29.375 176.005 4332 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.40 % Allowed : 8.76 % Favored : 89.84 % 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: 1.24 (0.27), residues: 983 helix: 1.72 (0.21), residues: 632 sheet: 0.54 (1.00), residues: 24 loop : -0.95 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 61 HIS 0.007 0.001 HIS E 113 PHE 0.014 0.002 PHE L 56 TYR 0.014 0.002 TYR C 50 ARG 0.005 0.000 ARG K 68 *********************** 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 117 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7801 (mt-10) REVERT: G 74 LYS cc_start: 0.8713 (mttp) cc_final: 0.8227 (mmtm) REVERT: L 28 ASP cc_start: 0.6356 (p0) cc_final: 0.6152 (t0) outliers start: 12 outliers final: 11 residues processed: 110 average time/residue: 0.3358 time to fit residues: 50.8452 Evaluate side-chains 113 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 0.0370 chunk 31 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14864 Z= 0.177 Angle : 0.536 8.898 21353 Z= 0.320 Chirality : 0.035 0.197 2419 Planarity : 0.005 0.058 1688 Dihedral : 29.307 176.070 4332 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.52 % Allowed : 9.93 % Favored : 88.55 % 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: 1.52 (0.27), residues: 983 helix: 1.95 (0.21), residues: 631 sheet: 0.67 (1.04), residues: 24 loop : -0.84 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 77 HIS 0.005 0.001 HIS L 75 PHE 0.025 0.002 PHE L 56 TYR 0.008 0.001 TYR H 37 ARG 0.005 0.000 ARG K 55 *********************** 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 118 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7757 (mt-10) REVERT: B 63 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7856 (mt-10) REVERT: G 74 LYS cc_start: 0.8723 (mttp) cc_final: 0.8225 (mmtm) REVERT: L 6 ILE cc_start: 0.7709 (mm) cc_final: 0.7345 (mm) outliers start: 13 outliers final: 12 residues processed: 110 average time/residue: 0.3214 time to fit residues: 48.6495 Evaluate side-chains 116 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 105 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14864 Z= 0.204 Angle : 0.531 6.853 21353 Z= 0.316 Chirality : 0.035 0.131 2419 Planarity : 0.004 0.048 1688 Dihedral : 29.261 176.711 4332 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.87 % Allowed : 10.28 % Favored : 87.85 % 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: 1.57 (0.27), residues: 983 helix: 2.00 (0.21), residues: 631 sheet: 0.71 (1.04), residues: 24 loop : -0.86 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 61 HIS 0.004 0.001 HIS L 75 PHE 0.017 0.001 PHE L 56 TYR 0.009 0.001 TYR D 40 ARG 0.008 0.000 ARG K 55 *********************** 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 121 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7762 (mt-10) REVERT: G 74 LYS cc_start: 0.8718 (mttp) cc_final: 0.8251 (mmtm) REVERT: L 6 ILE cc_start: 0.7365 (mm) cc_final: 0.6880 (mm) outliers start: 16 outliers final: 14 residues processed: 110 average time/residue: 0.3222 time to fit residues: 48.7134 Evaluate side-chains 119 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 105 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14864 Z= 0.184 Angle : 0.521 7.023 21353 Z= 0.312 Chirality : 0.034 0.130 2419 Planarity : 0.004 0.047 1688 Dihedral : 29.224 176.559 4332 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.22 % Allowed : 10.16 % 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: 1.61 (0.27), residues: 983 helix: 2.03 (0.21), residues: 631 sheet: 0.56 (1.03), residues: 24 loop : -0.83 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 77 HIS 0.004 0.001 HIS L 75 PHE 0.008 0.001 PHE B 61 TYR 0.009 0.001 TYR L 134 ARG 0.004 0.000 ARG K 55 *********************** 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 123 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: G 74 LYS cc_start: 0.8727 (mttp) cc_final: 0.8265 (mmtm) REVERT: L 6 ILE cc_start: 0.7398 (mm) cc_final: 0.6808 (mm) outliers start: 19 outliers final: 18 residues processed: 108 average time/residue: 0.3213 time to fit residues: 47.4464 Evaluate side-chains 122 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 105 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14864 Z= 0.288 Angle : 0.557 6.804 21353 Z= 0.329 Chirality : 0.037 0.138 2419 Planarity : 0.005 0.050 1688 Dihedral : 29.345 176.110 4332 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.34 % Allowed : 10.86 % Favored : 86.80 % 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: 1.35 (0.27), residues: 983 helix: 1.86 (0.21), residues: 632 sheet: 0.47 (1.00), residues: 24 loop : -1.02 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 61 HIS 0.006 0.001 HIS E 113 PHE 0.010 0.002 PHE L 56 TYR 0.009 0.001 TYR H 37 ARG 0.006 0.000 ARG K 55 *********************** 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 122 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7848 (mt-10) REVERT: C 92 GLU cc_start: 0.8793 (mp0) cc_final: 0.8197 (mt-10) REVERT: G 74 LYS cc_start: 0.8803 (mttp) cc_final: 0.8314 (mmtm) REVERT: L 6 ILE cc_start: 0.7763 (mm) cc_final: 0.7181 (mm) outliers start: 20 outliers final: 19 residues processed: 108 average time/residue: 0.3278 time to fit residues: 48.4396 Evaluate side-chains 120 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 105 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: 0.6980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14864 Z= 0.190 Angle : 0.538 7.067 21353 Z= 0.320 Chirality : 0.035 0.137 2419 Planarity : 0.005 0.083 1688 Dihedral : 29.331 175.772 4332 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.45 % Allowed : 10.98 % Favored : 86.57 % 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: 1.50 (0.27), residues: 983 helix: 1.99 (0.21), residues: 631 sheet: 0.51 (1.01), residues: 24 loop : -0.99 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 61 HIS 0.004 0.001 HIS L 75 PHE 0.009 0.001 PHE B 61 TYR 0.010 0.001 TYR D 40 ARG 0.005 0.000 ARG K 55 *********************** 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 125 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7815 (mt-10) REVERT: G 74 LYS cc_start: 0.8781 (mttp) cc_final: 0.8311 (mmtm) REVERT: L 6 ILE cc_start: 0.7859 (mm) cc_final: 0.7296 (mm) outliers start: 21 outliers final: 20 residues processed: 110 average time/residue: 0.3252 time to fit residues: 48.9142 Evaluate side-chains 124 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 111 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.0000 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 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: 0.6980 chunk 115 optimal weight: 7.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14864 Z= 0.210 Angle : 0.537 6.939 21353 Z= 0.320 Chirality : 0.035 0.135 2419 Planarity : 0.005 0.079 1688 Dihedral : 29.317 176.072 4332 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.34 % Allowed : 11.21 % Favored : 86.45 % 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: 1.97 (0.21), residues: 631 sheet: 0.51 (1.01), residues: 24 loop : -0.99 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 61 HIS 0.004 0.001 HIS L 75 PHE 0.009 0.001 PHE B 61 TYR 0.008 0.001 TYR D 40 ARG 0.015 0.000 ARG L 139 *********************** 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 124 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7819 (mt-10) REVERT: G 74 LYS cc_start: 0.8783 (mttp) cc_final: 0.8312 (mmtm) REVERT: L 6 ILE cc_start: 0.7859 (mm) cc_final: 0.7288 (mm) outliers start: 20 outliers final: 20 residues processed: 110 average time/residue: 0.3202 time to fit residues: 48.0544 Evaluate side-chains 124 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0845 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= 0.208 Angle : 0.536 7.011 21353 Z= 0.319 Chirality : 0.035 0.135 2419 Planarity : 0.005 0.092 1688 Dihedral : 29.313 176.071 4332 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.22 % Allowed : 11.21 % Favored : 86.57 % 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: 1.98 (0.21), residues: 631 sheet: 0.52 (1.01), residues: 24 loop : -0.98 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 61 HIS 0.004 0.001 HIS L 75 PHE 0.009 0.001 PHE B 61 TYR 0.009 0.001 TYR D 40 ARG 0.022 0.000 ARG L 139 ********************** 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 123 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7815 (mt-10) REVERT: G 74 LYS cc_start: 0.8782 (mttp) cc_final: 0.8312 (mmtm) REVERT: L 6 ILE cc_start: 0.7858 (mm) cc_final: 0.7288 (mm) outliers start: 19 outliers final: 19 residues processed: 110 average time/residue: 0.3243 time to fit residues: 48.7961 Evaluate side-chains 123 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 111 ASP 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: 0.9980 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.166512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114441 restraints weight = 23497.517| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.53 r_work: 0.2822 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0947 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= 0.284 Angle : 0.561 7.032 21353 Z= 0.331 Chirality : 0.037 0.140 2419 Planarity : 0.005 0.050 1688 Dihedral : 29.377 175.895 4332 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.34 % Allowed : 11.10 % Favored : 86.57 % 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: 1.29 (0.27), residues: 983 helix: 1.83 (0.21), residues: 632 sheet: 0.53 (1.01), residues: 24 loop : -1.10 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 61 HIS 0.006 0.001 HIS E 113 PHE 0.011 0.002 PHE B 61 TYR 0.008 0.001 TYR H 37 ARG 0.005 0.000 ARG K 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.89 seconds wall clock time: 44 minutes 1.92 seconds (2641.92 seconds total)