Starting phenix.real_space_refine on Tue Nov 18 18:50:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5z3v_6883/11_2025/5z3v_6883.cif Found real_map, /net/cci-nas-00/data/ceres_data/5z3v_6883/11_2025/5z3v_6883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5z3v_6883/11_2025/5z3v_6883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5z3v_6883/11_2025/5z3v_6883.map" model { file = "/net/cci-nas-00/data/ceres_data/5z3v_6883/11_2025/5z3v_6883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5z3v_6883/11_2025/5z3v_6883.cif" } resolution = 4.22 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 29 5.16 5 Be 1 3.05 5 C 9642 2.51 5 N 3087 2.21 5 O 3701 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16758 Number of models: 1 Model: "" Number of chains: 12 Chain: "O" Number of atoms: 4729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4729 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 559} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.17, per 1000 atoms: 0.25 Number of scatterers: 16758 At special positions: 0 Unit cell: (142.56, 130.68, 124.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 29 16.00 P 294 15.00 Mg 1 11.99 F 3 9.00 O 3701 8.00 N 3087 7.00 C 9642 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 533.8 milliseconds 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 13 sheets defined 65.3% alpha, 4.5% beta 145 base pairs and 238 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'O' and resid 672 through 689 Processing helix chain 'O' and resid 744 through 748 removed outlier: 3.653A pdb=" N ALA O 748 " --> pdb=" O TYR O 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 744 through 748' Processing helix chain 'O' and resid 769 through 784 removed outlier: 3.564A pdb=" N LYS O 773 " --> pdb=" O ASP O 769 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN O 784 " --> pdb=" O SER O 780 " (cutoff:3.500A) Processing helix chain 'O' and resid 797 through 813 Processing helix chain 'O' and resid 828 through 835 Processing helix chain 'O' and resid 850 through 861 removed outlier: 3.898A pdb=" N ARG O 854 " --> pdb=" O SER O 850 " (cutoff:3.500A) Processing helix chain 'O' and resid 862 through 864 No H-bonds generated for 'chain 'O' and resid 862 through 864' Processing helix chain 'O' and resid 874 through 879 Processing helix chain 'O' and resid 879 through 884 removed outlier: 3.720A pdb=" N SER O 884 " --> pdb=" O ARG O 880 " (cutoff:3.500A) Processing helix chain 'O' and resid 895 through 900 Processing helix chain 'O' and resid 904 through 911 removed outlier: 3.624A pdb=" N ASN O 911 " --> pdb=" O SER O 907 " (cutoff:3.500A) Processing helix chain 'O' and resid 933 through 942 Processing helix chain 'O' and resid 950 through 954 removed outlier: 4.159A pdb=" N ASP O 953 " --> pdb=" O LYS O 950 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU O 954 " --> pdb=" O SER O 951 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 950 through 954' Processing helix chain 'O' and resid 968 through 988 Processing helix chain 'O' and resid 995 through 1000 removed outlier: 3.784A pdb=" N VAL O 999 " --> pdb=" O LEU O 995 " (cutoff:3.500A) Processing helix chain 'O' and resid 1016 through 1030 removed outlier: 4.541A pdb=" N MET O1022 " --> pdb=" O LEU O1018 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR O1023 " --> pdb=" O GLN O1019 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN O1024 " --> pdb=" O GLN O1020 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG O1030 " --> pdb=" O MET O1026 " (cutoff:3.500A) Processing helix chain 'O' and resid 1049 through 1061 removed outlier: 4.158A pdb=" N LEU O1055 " --> pdb=" O GLN O1051 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS O1056 " --> pdb=" O ILE O1052 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS O1057 " --> pdb=" O MET O1053 " (cutoff:3.500A) Processing helix chain 'O' and resid 1065 through 1073 Processing helix chain 'O' and resid 1079 through 1083 removed outlier: 3.803A pdb=" N TRP O1083 " --> pdb=" O ASP O1080 " (cutoff:3.500A) Processing helix chain 'O' and resid 1087 through 1103 Proline residue: O1097 - end of helix Processing helix chain 'O' and resid 1113 through 1126 Processing helix chain 'O' and resid 1139 through 1150 removed outlier: 3.520A pdb=" N ASN O1150 " --> pdb=" O LEU O1146 " (cutoff:3.500A) Processing helix chain 'O' and resid 1163 through 1167 Processing helix chain 'O' and resid 1186 through 1195 removed outlier: 3.648A pdb=" N ASP O1190 " --> pdb=" O ASN O1186 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP O1195 " --> pdb=" O LEU O1191 " (cutoff:3.500A) Processing helix chain 'O' and resid 1217 through 1232 Processing helix chain 'O' and resid 1248 through 1269 removed outlier: 3.761A pdb=" N GLU O1269 " --> pdb=" O ARG O1265 " (cutoff:3.500A) Processing helix chain 'O' and resid 1279 through 1289 removed outlier: 3.827A pdb=" N ILE O1283 " --> pdb=" O LYS O1279 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE O1286 " --> pdb=" O GLU O1282 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU O1287 " --> pdb=" O ILE O1283 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG O1289 " --> pdb=" O GLU O1285 " (cutoff:3.500A) Processing helix chain 'O' and resid 1290 through 1297 Processing helix chain 'O' and resid 1298 through 1301 Processing helix chain 'O' and resid 1338 through 1347 Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.968A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.155A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.568A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.507A pdb=" N LEU C 116 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.968A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 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: 3.880A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.697A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.568A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 98 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.507A pdb=" N LEU G 116 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing sheet with id=AA1, first strand: chain 'O' and resid 789 through 790 removed outlier: 7.923A pdb=" N LEU O 922 " --> pdb=" O MET O 891 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE O 893 " --> pdb=" O LEU O 922 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 789 through 790 removed outlier: 7.923A pdb=" N LEU O 922 " --> pdb=" O MET O 891 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE O 893 " --> pdb=" O LEU O 922 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL O 889 " --> pdb=" O ALA O 916 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 1160 through 1162 removed outlier: 3.686A pdb=" N LEU O1161 " --> pdb=" O ILE O1108 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE O1110 " --> pdb=" O LEU O1161 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL O1178 " --> pdb=" O LEU O1209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.769A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.522A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.235A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.198A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.676A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB3, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.211A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 77 through 78 599 hydrogen bonds defined for protein. 1773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 238 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 1.92 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: 3687 1.33 - 1.45: 4803 1.45 - 1.57: 8509 1.57 - 1.69: 585 1.69 - 1.81: 56 Bond restraints: 17640 Sorted by residual: bond pdb=" F2 BEF O1502 " pdb="BE BEF O1502 " ideal model delta sigma weight residual 1.476 1.709 -0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" F1 BEF O1502 " pdb="BE BEF O1502 " ideal model delta sigma weight residual 1.476 1.705 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" F3 BEF O1502 " pdb="BE BEF O1502 " ideal model delta sigma weight residual 1.476 1.689 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.17e+00 ... (remaining 17635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 25010 4.14 - 8.29: 49 8.29 - 12.43: 4 12.43 - 16.58: 1 16.58 - 20.72: 1 Bond angle restraints: 25065 Sorted by residual: angle pdb=" F1 BEF O1502 " pdb="BE BEF O1502 " pdb=" F3 BEF O1502 " ideal model delta sigma weight residual 120.12 99.40 20.72 3.00e+00 1.11e-01 4.77e+01 angle pdb=" N PRO O 959 " pdb=" CA PRO O 959 " pdb=" CB PRO O 959 " ideal model delta sigma weight residual 103.25 110.03 -6.78 1.05e+00 9.07e-01 4.16e+01 angle pdb=" F2 BEF O1502 " pdb="BE BEF O1502 " pdb=" F3 BEF O1502 " ideal model delta sigma weight residual 119.96 104.79 15.17 3.00e+00 1.11e-01 2.56e+01 angle pdb=" CA THR O 958 " pdb=" C THR O 958 " pdb=" N PRO O 959 " ideal model delta sigma weight residual 120.77 117.09 3.68 9.70e-01 1.06e+00 1.44e+01 angle pdb=" C GLU O 793 " pdb=" N MET O 794 " pdb=" CA MET O 794 " ideal model delta sigma weight residual 122.19 130.80 -8.61 2.30e+00 1.89e-01 1.40e+01 ... (remaining 25060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 8557 33.91 - 67.82: 1343 67.82 - 101.73: 14 101.73 - 135.65: 1 135.65 - 169.56: 2 Dihedral angle restraints: 9917 sinusoidal: 6007 harmonic: 3910 Sorted by residual: dihedral pdb=" CA TYR O 810 " pdb=" C TYR O 810 " pdb=" N GLU O 811 " pdb=" CA GLU O 811 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA SER O 951 " pdb=" C SER O 951 " pdb=" N PHE O 952 " pdb=" CA PHE O 952 " ideal model delta harmonic sigma weight residual -180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA PHE O1110 " pdb=" C PHE O1110 " pdb=" N GLN O1111 " pdb=" CA GLN O1111 " ideal model delta harmonic sigma weight residual 180.00 157.92 22.08 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 9914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2368 0.046 - 0.092: 397 0.092 - 0.138: 81 0.138 - 0.184: 4 0.184 - 0.230: 4 Chirality restraints: 2854 Sorted by residual: chirality pdb=" CA PRO O 959 " pdb=" N PRO O 959 " pdb=" C PRO O 959 " pdb=" CB PRO O 959 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ASP O1184 " pdb=" N ASP O1184 " pdb=" C ASP O1184 " pdb=" CB ASP O1184 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CG LEU O 820 " pdb=" CB LEU O 820 " pdb=" CD1 LEU O 820 " pdb=" CD2 LEU O 820 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.04e-01 ... (remaining 2851 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 48 " -0.019 2.00e-02 2.50e+03 1.51e-02 5.68e+00 pdb=" N1 DT I 48 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DT I 48 " 0.032 2.00e-02 2.50e+03 pdb=" O2 DT I 48 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 48 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 48 " -0.024 2.00e-02 2.50e+03 pdb=" O4 DT I 48 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DT I 48 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 48 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DT I 48 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN O1073 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO O1074 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO O1074 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO O1074 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 100 " 0.017 2.00e-02 2.50e+03 1.33e-02 4.88e+00 pdb=" N9 DA J 100 " -0.008 2.00e-02 2.50e+03 pdb=" C8 DA J 100 " -0.008 2.00e-02 2.50e+03 pdb=" N7 DA J 100 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DA J 100 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA J 100 " 0.030 2.00e-02 2.50e+03 pdb=" N6 DA J 100 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DA J 100 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA J 100 " -0.023 2.00e-02 2.50e+03 pdb=" N3 DA J 100 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA J 100 " -0.003 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 762 2.71 - 3.26: 15706 3.26 - 3.80: 30302 3.80 - 4.35: 38337 4.35 - 4.90: 55758 Nonbonded interactions: 140865 Sorted by model distance: nonbonded pdb=" O3B ADP O1501 " pdb=" F3 BEF O1502 " model vdw 2.160 2.990 nonbonded pdb=" O ARG O 880 " pdb=" OG SER O 884 " model vdw 2.170 3.040 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.179 3.040 nonbonded pdb=" O2A ADP O1501 " pdb=" F3 BEF O1502 " model vdw 2.179 2.990 nonbonded pdb=" O ASP O1301 " pdb=" OG SER O1305 " model vdw 2.188 3.040 ... (remaining 140860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and ((resid 20 and (name N or name CA or name C or name O or name CB \ )) or resid 21 through 101)) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.450 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.233 17640 Z= 0.204 Angle : 0.630 20.720 25065 Z= 0.364 Chirality : 0.037 0.230 2854 Planarity : 0.004 0.058 2160 Dihedral : 22.976 169.558 7377 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.20), residues: 1309 helix: -1.72 (0.16), residues: 793 sheet: -2.78 (0.49), residues: 54 loop : -1.47 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 993 TYR 0.035 0.002 TYR O 810 PHE 0.028 0.002 PHE O 946 TRP 0.019 0.002 TRP O 955 HIS 0.006 0.001 HIS O 984 Details of bonding type rmsd covalent geometry : bond 0.00410 (17640) covalent geometry : angle 0.62984 (25065) hydrogen bonds : bond 0.11863 ( 970) hydrogen bonds : angle 8.13508 ( 2517) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 762 LEU cc_start: 0.6456 (tp) cc_final: 0.5683 (mt) REVERT: O 770 TYR cc_start: 0.6638 (p90) cc_final: 0.6227 (p90) REVERT: O 792 ASP cc_start: 0.7165 (p0) cc_final: 0.6468 (p0) REVERT: O 809 LEU cc_start: 0.5287 (mt) cc_final: 0.4960 (mt) REVERT: O 812 MET cc_start: 0.6557 (mtm) cc_final: 0.5778 (mmp) REVERT: O 852 ASN cc_start: 0.8762 (m110) cc_final: 0.8555 (m-40) REVERT: O 899 MET cc_start: 0.6788 (tpt) cc_final: 0.6488 (tpp) REVERT: O 981 ARG cc_start: 0.6569 (mtm-85) cc_final: 0.6273 (tpp80) REVERT: O 1024 GLN cc_start: 0.7364 (mp10) cc_final: 0.6397 (tm-30) REVERT: O 1115 ILE cc_start: 0.8583 (mp) cc_final: 0.8285 (tt) REVERT: O 1132 ARG cc_start: 0.8339 (ptm-80) cc_final: 0.7865 (tmm160) REVERT: O 1140 ASP cc_start: 0.8112 (m-30) cc_final: 0.7237 (t0) REVERT: O 1160 ILE cc_start: 0.7703 (mt) cc_final: 0.7462 (mp) REVERT: O 1285 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7635 (tm-30) REVERT: A 81 ASP cc_start: 0.8924 (m-30) cc_final: 0.8652 (m-30) REVERT: A 129 ARG cc_start: 0.6945 (tpt90) cc_final: 0.6706 (tpt170) REVERT: A 131 ARG cc_start: 0.6995 (mtt180) cc_final: 0.6768 (mtt90) REVERT: B 25 ASN cc_start: 0.8702 (m-40) cc_final: 0.8342 (m110) REVERT: C 84 GLN cc_start: 0.7920 (tp40) cc_final: 0.7609 (tp40) REVERT: C 99 ARG cc_start: 0.7731 (mtt-85) cc_final: 0.7028 (mtp85) REVERT: C 108 LEU cc_start: 0.8074 (mt) cc_final: 0.7708 (mt) REVERT: E 42 ARG cc_start: 0.7541 (ttm170) cc_final: 0.7128 (mtp85) REVERT: E 79 LYS cc_start: 0.7923 (tttp) cc_final: 0.7608 (ttpt) REVERT: E 90 MET cc_start: 0.8054 (mmm) cc_final: 0.7293 (mmt) REVERT: F 72 TYR cc_start: 0.8378 (m-80) cc_final: 0.8013 (m-80) REVERT: F 91 LYS cc_start: 0.8588 (tttt) cc_final: 0.8382 (ttpt) REVERT: F 93 GLN cc_start: 0.7325 (mt0) cc_final: 0.7098 (mt0) REVERT: G 64 GLU cc_start: 0.7964 (tt0) cc_final: 0.7540 (tt0) REVERT: G 94 ASN cc_start: 0.8134 (t0) cc_final: 0.7880 (t0) REVERT: G 95 LYS cc_start: 0.7487 (tptm) cc_final: 0.6944 (mtpt) REVERT: G 104 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8743 (mm-40) REVERT: H 33 SER cc_start: 0.8514 (t) cc_final: 0.8263 (p) REVERT: H 42 LEU cc_start: 0.8694 (tp) cc_final: 0.8433 (tt) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.2110 time to fit residues: 101.6583 Evaluate side-chains 193 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 681 HIS O 749 HIS O 787 ASN O 913 HIS O 915 HIS ** O1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1025 GLN O1071 GLN O1104 HIS A 39 HIS A 68 GLN B 25 ASN D 46 HIS D 79 HIS D 81 ASN E 68 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.142314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120638 restraints weight = 27191.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119515 restraints weight = 57287.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119670 restraints weight = 54079.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.119162 restraints weight = 42626.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.119231 restraints weight = 43161.353| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17640 Z= 0.194 Angle : 0.648 8.977 25065 Z= 0.362 Chirality : 0.039 0.176 2854 Planarity : 0.005 0.093 2160 Dihedral : 28.054 174.075 4676 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.22), residues: 1309 helix: -0.11 (0.18), residues: 813 sheet: -2.29 (0.55), residues: 55 loop : -1.27 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O1316 TYR 0.026 0.002 TYR O 810 PHE 0.023 0.002 PHE O1159 TRP 0.016 0.002 TRP O 777 HIS 0.006 0.001 HIS O 984 Details of bonding type rmsd covalent geometry : bond 0.00435 (17640) covalent geometry : angle 0.64755 (25065) hydrogen bonds : bond 0.04863 ( 970) hydrogen bonds : angle 4.92810 ( 2517) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 850 SER cc_start: 0.7263 (p) cc_final: 0.6754 (p) REVERT: O 943 PRO cc_start: 0.2323 (Cg_exo) cc_final: 0.2085 (Cg_endo) REVERT: O 1024 GLN cc_start: 0.6422 (mp10) cc_final: 0.5733 (tm-30) REVERT: O 1061 HIS cc_start: 0.4220 (m-70) cc_final: 0.3861 (m-70) REVERT: O 1115 ILE cc_start: 0.7955 (mp) cc_final: 0.7616 (mm) REVERT: O 1140 ASP cc_start: 0.6620 (m-30) cc_final: 0.6417 (t0) REVERT: O 1160 ILE cc_start: 0.8205 (mt) cc_final: 0.7893 (mp) REVERT: O 1214 THR cc_start: 0.4874 (p) cc_final: 0.4573 (p) REVERT: C 108 LEU cc_start: 0.8125 (mt) cc_final: 0.7899 (mt) REVERT: D 79 HIS cc_start: 0.7635 (OUTLIER) cc_final: 0.7342 (t-90) REVERT: D 103 LEU cc_start: 0.8687 (mt) cc_final: 0.8487 (mt) REVERT: E 79 LYS cc_start: 0.8239 (tttp) cc_final: 0.7606 (ttmm) REVERT: E 90 MET cc_start: 0.7440 (mmm) cc_final: 0.6466 (mmt) REVERT: E 129 ARG cc_start: 0.7421 (tpt-90) cc_final: 0.6454 (tpt90) REVERT: F 72 TYR cc_start: 0.8086 (m-80) cc_final: 0.7795 (m-80) REVERT: F 91 LYS cc_start: 0.8327 (tttt) cc_final: 0.8099 (ttpp) REVERT: G 95 LYS cc_start: 0.7630 (tptm) cc_final: 0.7236 (mtpt) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.1805 time to fit residues: 58.7784 Evaluate side-chains 165 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 129 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 86 optimal weight: 0.0370 chunk 154 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 5 optimal weight: 0.2980 chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 776 GLN O 787 ASN O1071 GLN D 81 ASN F 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.147000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124473 restraints weight = 26911.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.123418 restraints weight = 49808.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.124001 restraints weight = 49149.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.123349 restraints weight = 38932.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.123699 restraints weight = 40985.242| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17640 Z= 0.139 Angle : 0.581 8.372 25065 Z= 0.328 Chirality : 0.036 0.165 2854 Planarity : 0.005 0.086 2160 Dihedral : 27.787 175.366 4676 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.09 % Allowed : 1.57 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.23), residues: 1309 helix: 0.88 (0.18), residues: 818 sheet: -1.85 (0.55), residues: 60 loop : -0.99 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.018 0.002 TYR O 810 PHE 0.017 0.001 PHE O1241 TRP 0.021 0.002 TRP O 777 HIS 0.006 0.001 HIS O 681 Details of bonding type rmsd covalent geometry : bond 0.00290 (17640) covalent geometry : angle 0.58051 (25065) hydrogen bonds : bond 0.03861 ( 970) hydrogen bonds : angle 4.22639 ( 2517) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1024 GLN cc_start: 0.6355 (mp10) cc_final: 0.6040 (tp40) REVERT: O 1115 ILE cc_start: 0.8161 (mp) cc_final: 0.7955 (mm) REVERT: O 1140 ASP cc_start: 0.6636 (m-30) cc_final: 0.6423 (t0) REVERT: O 1160 ILE cc_start: 0.8270 (mt) cc_final: 0.7837 (mp) REVERT: A 115 LYS cc_start: 0.7896 (mmtm) cc_final: 0.7671 (mmmm) REVERT: B 74 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7220 (mt-10) REVERT: D 68 GLU cc_start: 0.6700 (tt0) cc_final: 0.6391 (tt0) REVERT: E 79 LYS cc_start: 0.8221 (tttp) cc_final: 0.7608 (ttmm) REVERT: E 90 MET cc_start: 0.7210 (mmm) cc_final: 0.6645 (mmt) REVERT: E 129 ARG cc_start: 0.7360 (tpt-90) cc_final: 0.6531 (tpt90) REVERT: F 91 LYS cc_start: 0.8034 (tttt) cc_final: 0.7825 (ttpp) REVERT: G 61 GLU cc_start: 0.7857 (tp30) cc_final: 0.7616 (tp30) REVERT: G 84 GLN cc_start: 0.8020 (tp40) cc_final: 0.7560 (tp40) REVERT: G 92 GLU cc_start: 0.7913 (mp0) cc_final: 0.7652 (mp0) REVERT: G 95 LYS cc_start: 0.7501 (tptm) cc_final: 0.7212 (mtpt) REVERT: H 85 THR cc_start: 0.9162 (t) cc_final: 0.8924 (p) outliers start: 1 outliers final: 1 residues processed: 230 average time/residue: 0.1532 time to fit residues: 50.9674 Evaluate side-chains 156 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 130 optimal weight: 10.0000 chunk 3 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 153 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 787 ASN O 913 HIS ** O1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1237 GLN A 39 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS F 93 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.139903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116648 restraints weight = 27414.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115561 restraints weight = 63408.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115764 restraints weight = 57358.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115430 restraints weight = 42439.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.115605 restraints weight = 42020.242| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17640 Z= 0.276 Angle : 0.694 9.177 25065 Z= 0.385 Chirality : 0.042 0.180 2854 Planarity : 0.005 0.065 2160 Dihedral : 28.366 175.240 4676 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1309 helix: 0.77 (0.18), residues: 809 sheet: -1.95 (0.59), residues: 60 loop : -1.11 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 116 TYR 0.024 0.002 TYR O 810 PHE 0.023 0.002 PHE O1159 TRP 0.019 0.002 TRP O 777 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00638 (17640) covalent geometry : angle 0.69360 (25065) hydrogen bonds : bond 0.05293 ( 970) hydrogen bonds : angle 4.43478 ( 2517) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1009 LYS cc_start: 0.6908 (mmtt) cc_final: 0.6627 (tttp) REVERT: O 1115 ILE cc_start: 0.8036 (mp) cc_final: 0.7829 (mm) REVERT: O 1158 CYS cc_start: 0.8068 (p) cc_final: 0.7792 (p) REVERT: O 1160 ILE cc_start: 0.8407 (mt) cc_final: 0.7934 (mp) REVERT: O 1349 ARG cc_start: 0.2355 (mmt-90) cc_final: 0.1402 (ptm160) REVERT: B 27 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7344 (mp10) REVERT: B 74 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7316 (mt-10) REVERT: D 68 GLU cc_start: 0.6857 (tt0) cc_final: 0.6606 (tt0) REVERT: E 79 LYS cc_start: 0.8328 (tttp) cc_final: 0.7560 (ttmm) REVERT: E 129 ARG cc_start: 0.7528 (tpt-90) cc_final: 0.6651 (tpt90) REVERT: F 27 GLN cc_start: 0.8631 (mm110) cc_final: 0.8332 (mm110) REVERT: F 44 LYS cc_start: 0.8360 (mtpt) cc_final: 0.8044 (mtpt) REVERT: G 95 LYS cc_start: 0.7481 (tptm) cc_final: 0.7158 (mtpt) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1536 time to fit residues: 45.9328 Evaluate side-chains 159 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 19 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 785 HIS O 787 ASN ** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1019 GLN O1050 ASN O1071 GLN ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS F 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.139865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116976 restraints weight = 27326.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.116392 restraints weight = 59588.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116796 restraints weight = 59311.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116084 restraints weight = 48481.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116130 restraints weight = 49604.081| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17640 Z= 0.236 Angle : 0.655 8.032 25065 Z= 0.367 Chirality : 0.040 0.185 2854 Planarity : 0.005 0.053 2160 Dihedral : 28.303 175.440 4676 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.23), residues: 1309 helix: 0.79 (0.18), residues: 821 sheet: -1.83 (0.60), residues: 61 loop : -1.21 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 919 TYR 0.023 0.002 TYR O 810 PHE 0.022 0.002 PHE O1159 TRP 0.022 0.002 TRP O 777 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00542 (17640) covalent geometry : angle 0.65487 (25065) hydrogen bonds : bond 0.04974 ( 970) hydrogen bonds : angle 4.26518 ( 2517) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 825 LEU cc_start: 0.8722 (tt) cc_final: 0.8480 (tp) REVERT: O 1009 LYS cc_start: 0.7422 (mmtt) cc_final: 0.7174 (tttp) REVERT: O 1115 ILE cc_start: 0.8096 (mp) cc_final: 0.7758 (mp) REVERT: O 1150 ASN cc_start: 0.7672 (m110) cc_final: 0.6727 (t0) REVERT: O 1349 ARG cc_start: 0.2490 (mmt-90) cc_final: 0.1534 (ptm160) REVERT: B 27 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7454 (mp10) REVERT: B 74 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7287 (mt-10) REVERT: C 15 LYS cc_start: 0.7297 (ttmt) cc_final: 0.6556 (mtpt) REVERT: C 75 LYS cc_start: 0.7674 (mmtt) cc_final: 0.7453 (mtmt) REVERT: E 79 LYS cc_start: 0.8347 (tttp) cc_final: 0.7601 (ttmm) REVERT: E 90 MET cc_start: 0.7017 (mmp) cc_final: 0.6711 (mmt) REVERT: E 129 ARG cc_start: 0.7494 (tpt-90) cc_final: 0.6508 (tpt90) REVERT: F 27 GLN cc_start: 0.8635 (mm110) cc_final: 0.8380 (mm110) REVERT: F 44 LYS cc_start: 0.8382 (mtpt) cc_final: 0.8098 (mtpt) REVERT: G 92 GLU cc_start: 0.8313 (mp0) cc_final: 0.7959 (mp0) REVERT: G 95 LYS cc_start: 0.7463 (tptm) cc_final: 0.7219 (mtpt) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1447 time to fit residues: 42.6405 Evaluate side-chains 157 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 776 GLN O1071 GLN B 75 HIS D 81 ASN F 18 HIS F 93 GLN G 38 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.143989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.122118 restraints weight = 27188.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.121636 restraints weight = 50584.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.121705 restraints weight = 46107.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.121317 restraints weight = 38625.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.121336 restraints weight = 35795.277| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17640 Z= 0.142 Angle : 0.579 9.107 25065 Z= 0.328 Chirality : 0.036 0.170 2854 Planarity : 0.004 0.050 2160 Dihedral : 27.894 175.358 4676 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.23), residues: 1309 helix: 1.30 (0.19), residues: 831 sheet: -1.15 (0.68), residues: 55 loop : -1.09 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 96 TYR 0.021 0.002 TYR D 80 PHE 0.018 0.002 PHE O1159 TRP 0.025 0.002 TRP O 777 HIS 0.007 0.001 HIS O1061 Details of bonding type rmsd covalent geometry : bond 0.00305 (17640) covalent geometry : angle 0.57943 (25065) hydrogen bonds : bond 0.03915 ( 970) hydrogen bonds : angle 3.87275 ( 2517) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 825 LEU cc_start: 0.8651 (tt) cc_final: 0.8346 (tp) REVERT: O 1150 ASN cc_start: 0.7556 (m110) cc_final: 0.6665 (t0) REVERT: O 1349 ARG cc_start: 0.2494 (mmt-90) cc_final: 0.1404 (ptm160) REVERT: A 115 LYS cc_start: 0.8198 (mmtm) cc_final: 0.7819 (mmmm) REVERT: B 27 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7288 (mp10) REVERT: B 74 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7009 (mt-10) REVERT: B 79 LYS cc_start: 0.8190 (mttm) cc_final: 0.7878 (mtpp) REVERT: C 75 LYS cc_start: 0.7622 (mmtt) cc_final: 0.7361 (mtmt) REVERT: E 79 LYS cc_start: 0.8364 (tttp) cc_final: 0.7684 (ttmm) REVERT: E 90 MET cc_start: 0.7037 (mmp) cc_final: 0.6769 (mmt) REVERT: E 129 ARG cc_start: 0.7390 (tpt-90) cc_final: 0.6514 (tpt90) REVERT: F 18 HIS cc_start: 0.5651 (t-90) cc_final: 0.5282 (t70) REVERT: G 50 TYR cc_start: 0.8996 (t80) cc_final: 0.8478 (t80) REVERT: G 95 LYS cc_start: 0.7480 (tptm) cc_final: 0.7168 (mtpt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1514 time to fit residues: 45.0763 Evaluate side-chains 162 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 55 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 100 optimal weight: 0.1980 chunk 3 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 49 optimal weight: 0.0000 chunk 142 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 overall best weight: 3.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.140967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.118974 restraints weight = 27389.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118182 restraints weight = 51915.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.117837 restraints weight = 50219.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.117251 restraints weight = 42280.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117156 restraints weight = 39911.501| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17640 Z= 0.203 Angle : 0.635 8.560 25065 Z= 0.357 Chirality : 0.039 0.177 2854 Planarity : 0.004 0.052 2160 Dihedral : 28.185 175.084 4676 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.09 % Allowed : 1.40 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.23), residues: 1309 helix: 1.15 (0.18), residues: 827 sheet: -1.29 (0.69), residues: 54 loop : -1.27 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 42 TYR 0.025 0.002 TYR O 810 PHE 0.019 0.002 PHE O1159 TRP 0.024 0.002 TRP O 777 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00466 (17640) covalent geometry : angle 0.63493 (25065) hydrogen bonds : bond 0.04661 ( 970) hydrogen bonds : angle 4.07335 ( 2517) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 825 LEU cc_start: 0.8624 (tt) cc_final: 0.8398 (tp) REVERT: O 1150 ASN cc_start: 0.7594 (m110) cc_final: 0.6712 (t0) REVERT: O 1215 ASN cc_start: 0.8324 (m-40) cc_final: 0.7882 (m-40) REVERT: O 1349 ARG cc_start: 0.2463 (mmt-90) cc_final: 0.1475 (ptm160) REVERT: B 74 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7179 (mt-10) REVERT: C 15 LYS cc_start: 0.7351 (ttmt) cc_final: 0.6577 (mtpt) REVERT: D 82 LYS cc_start: 0.8522 (mttm) cc_final: 0.8278 (mttm) REVERT: E 79 LYS cc_start: 0.8459 (tttp) cc_final: 0.7769 (ttmm) REVERT: E 90 MET cc_start: 0.7059 (mmp) cc_final: 0.6833 (mmt) REVERT: E 129 ARG cc_start: 0.7538 (tpt-90) cc_final: 0.6515 (tpt90) REVERT: F 18 HIS cc_start: 0.5608 (t-90) cc_final: 0.5333 (t70) REVERT: G 92 GLU cc_start: 0.8185 (mp0) cc_final: 0.7936 (mp0) REVERT: G 95 LYS cc_start: 0.7501 (tptm) cc_final: 0.7136 (mtpt) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.1532 time to fit residues: 44.1404 Evaluate side-chains 158 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 19 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 785 HIS O1071 GLN O1194 GLN D 81 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.141651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.119819 restraints weight = 27764.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119151 restraints weight = 50840.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119020 restraints weight = 47320.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118245 restraints weight = 43041.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118278 restraints weight = 38342.974| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17640 Z= 0.174 Angle : 0.617 8.541 25065 Z= 0.346 Chirality : 0.038 0.227 2854 Planarity : 0.004 0.051 2160 Dihedral : 28.061 174.198 4676 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.09 % Allowed : 1.22 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.23), residues: 1309 helix: 1.27 (0.18), residues: 827 sheet: -1.25 (0.68), residues: 54 loop : -1.38 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 71 TYR 0.019 0.002 TYR H 80 PHE 0.026 0.002 PHE O1110 TRP 0.027 0.002 TRP O 777 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00390 (17640) covalent geometry : angle 0.61675 (25065) hydrogen bonds : bond 0.04261 ( 970) hydrogen bonds : angle 3.97629 ( 2517) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 825 LEU cc_start: 0.8638 (tt) cc_final: 0.8405 (tp) REVERT: O 1157 LEU cc_start: 0.7899 (pt) cc_final: 0.6965 (mt) REVERT: O 1214 THR cc_start: 0.4475 (p) cc_final: 0.4269 (p) REVERT: O 1215 ASN cc_start: 0.8079 (m-40) cc_final: 0.7493 (m-40) REVERT: O 1349 ARG cc_start: 0.2601 (mmt-90) cc_final: 0.1459 (ptm160) REVERT: B 27 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7326 (mp10) REVERT: B 74 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7251 (mt-10) REVERT: C 15 LYS cc_start: 0.7335 (ttmt) cc_final: 0.6570 (mtpt) REVERT: C 75 LYS cc_start: 0.7669 (mtmt) cc_final: 0.7364 (mtmm) REVERT: D 82 LYS cc_start: 0.8517 (mttm) cc_final: 0.8284 (mttm) REVERT: E 79 LYS cc_start: 0.8424 (tttp) cc_final: 0.7778 (ttmm) REVERT: E 129 ARG cc_start: 0.7584 (tpt-90) cc_final: 0.6501 (tpt90) REVERT: F 18 HIS cc_start: 0.5756 (t-90) cc_final: 0.5382 (t70) REVERT: G 73 ASN cc_start: 0.7060 (OUTLIER) cc_final: 0.6647 (t160) REVERT: G 92 GLU cc_start: 0.8208 (mp0) cc_final: 0.7947 (mp0) REVERT: G 95 LYS cc_start: 0.7429 (tptm) cc_final: 0.7171 (mtpt) REVERT: G 100 VAL cc_start: 0.8371 (t) cc_final: 0.7933 (p) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1446 time to fit residues: 41.1759 Evaluate side-chains 156 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 119 optimal weight: 0.0770 chunk 137 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 681 HIS O1071 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.143930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.121892 restraints weight = 27479.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121297 restraints weight = 54743.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121038 restraints weight = 54273.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120252 restraints weight = 45720.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.120445 restraints weight = 41146.613| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17640 Z= 0.147 Angle : 0.590 8.125 25065 Z= 0.331 Chirality : 0.036 0.196 2854 Planarity : 0.004 0.047 2160 Dihedral : 27.881 173.800 4676 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1309 helix: 1.50 (0.19), residues: 827 sheet: -0.82 (0.74), residues: 48 loop : -1.39 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 71 TYR 0.017 0.002 TYR O1226 PHE 0.023 0.002 PHE O1110 TRP 0.032 0.002 TRP O 777 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00319 (17640) covalent geometry : angle 0.59000 (25065) hydrogen bonds : bond 0.03880 ( 970) hydrogen bonds : angle 3.75876 ( 2517) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 825 LEU cc_start: 0.8611 (tt) cc_final: 0.8352 (tp) REVERT: O 1150 ASN cc_start: 0.7775 (m110) cc_final: 0.6994 (t0) REVERT: O 1157 LEU cc_start: 0.7718 (pt) cc_final: 0.6755 (mt) REVERT: O 1215 ASN cc_start: 0.8170 (m-40) cc_final: 0.7732 (m-40) REVERT: O 1349 ARG cc_start: 0.2498 (mmt-90) cc_final: 0.1347 (ptm160) REVERT: B 27 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7231 (mp10) REVERT: C 15 LYS cc_start: 0.7281 (ttmt) cc_final: 0.6502 (mtpt) REVERT: C 75 LYS cc_start: 0.7933 (mtmt) cc_final: 0.7720 (mtmm) REVERT: E 79 LYS cc_start: 0.8319 (tttp) cc_final: 0.8016 (ttmm) REVERT: E 90 MET cc_start: 0.6964 (mmt) cc_final: 0.6700 (mmt) REVERT: E 129 ARG cc_start: 0.7510 (tpt-90) cc_final: 0.6640 (tpt90) REVERT: F 18 HIS cc_start: 0.5825 (t-90) cc_final: 0.5416 (t70) REVERT: G 50 TYR cc_start: 0.9089 (t80) cc_final: 0.8553 (t80) REVERT: G 95 LYS cc_start: 0.7421 (tptm) cc_final: 0.7108 (mtpt) REVERT: G 100 VAL cc_start: 0.8393 (t) cc_final: 0.7965 (p) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1470 time to fit residues: 41.1349 Evaluate side-chains 162 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 116 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 785 HIS O1019 GLN O1071 GLN O1171 ASN ** O1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.138669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111979 restraints weight = 28299.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110397 restraints weight = 56895.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111041 restraints weight = 54468.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.110732 restraints weight = 39514.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110737 restraints weight = 43898.331| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 17640 Z= 0.304 Angle : 0.732 9.519 25065 Z= 0.405 Chirality : 0.044 0.234 2854 Planarity : 0.005 0.057 2160 Dihedral : 28.555 173.739 4676 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.23), residues: 1309 helix: 1.02 (0.18), residues: 818 sheet: -1.53 (0.66), residues: 54 loop : -1.49 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.021 0.002 TYR D 80 PHE 0.030 0.003 PHE O1159 TRP 0.019 0.002 TRP O 777 HIS 0.009 0.002 HIS O 785 Details of bonding type rmsd covalent geometry : bond 0.00706 (17640) covalent geometry : angle 0.73182 (25065) hydrogen bonds : bond 0.05515 ( 970) hydrogen bonds : angle 4.20010 ( 2517) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 825 LEU cc_start: 0.8735 (tt) cc_final: 0.8522 (tp) REVERT: O 1026 MET cc_start: 0.5521 (mmp) cc_final: 0.5248 (tpt) REVERT: O 1349 ARG cc_start: 0.2276 (mmt-90) cc_final: 0.1278 (ptm160) REVERT: B 27 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7351 (mp10) REVERT: C 15 LYS cc_start: 0.7446 (ttmt) cc_final: 0.7053 (ttmt) REVERT: C 108 LEU cc_start: 0.8327 (mt) cc_final: 0.8105 (mt) REVERT: D 32 GLU cc_start: 0.5985 (pp20) cc_final: 0.5744 (pp20) REVERT: E 79 LYS cc_start: 0.8472 (tttp) cc_final: 0.7772 (ttmm) REVERT: E 90 MET cc_start: 0.6840 (mmt) cc_final: 0.6602 (mmt) REVERT: E 129 ARG cc_start: 0.7581 (tpt-90) cc_final: 0.6523 (tpt90) REVERT: F 18 HIS cc_start: 0.6313 (t-90) cc_final: 0.6006 (t70) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1411 time to fit residues: 40.5905 Evaluate side-chains 158 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 56 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 0.0670 chunk 84 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O1071 GLN O1171 ASN D 46 HIS F 25 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113422 restraints weight = 27990.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.112256 restraints weight = 52567.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112832 restraints weight = 53542.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.112790 restraints weight = 36343.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.112763 restraints weight = 42560.738| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17640 Z= 0.208 Angle : 0.654 9.968 25065 Z= 0.365 Chirality : 0.039 0.203 2854 Planarity : 0.005 0.054 2160 Dihedral : 28.308 172.321 4676 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.23), residues: 1309 helix: 1.13 (0.18), residues: 825 sheet: -1.48 (0.65), residues: 54 loop : -1.56 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 71 TYR 0.042 0.002 TYR H 80 PHE 0.024 0.002 PHE O1159 TRP 0.026 0.002 TRP O 777 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00477 (17640) covalent geometry : angle 0.65385 (25065) hydrogen bonds : bond 0.04673 ( 970) hydrogen bonds : angle 4.01521 ( 2517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2094.77 seconds wall clock time: 37 minutes 11.21 seconds (2231.21 seconds total)