Starting phenix.real_space_refine on Sun Oct 25 08:50:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5z3v_6883/10_2026/5z3v_6883.cif Found real_map, /net/cci-nas-00/data/ceres_data/5z3v_6883/10_2026/5z3v_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_6883/10_2026/5z3v_6883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5z3v_6883/10_2026/5z3v_6883.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5z3v_6883/10_2026/5z3v_6883.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5z3v_6883/10_2026/5z3v_6883.cif" model { file = "/net/cci-nas-00/data/ceres_data/5z3v_6883/10_2026/5z3v_6883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5z3v_6883/10_2026/5z3v_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-2.3rc1-6221/lib/python3.11/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: 3.11, per 1000 atoms: 0.19 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: 1.43 Conformation dependent library (CDL) restraints added in 592.5 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: 2.27 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: 4.47 Time building geometry restraints manager: 1.85 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 7 " pdb=" C2' DT J 7 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DC I 74 " pdb=" C2' DC I 74 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 ... (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=" O4' DT I 48 " pdb=" C4' DT I 48 " pdb=" C3' DT I 48 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.35e+01 angle pdb=" N3 DT I 35 " pdb=" C4 DT I 35 " pdb=" O4 DT I 35 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+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: 2141 0.046 - 0.092: 562 0.092 - 0.138: 142 0.138 - 0.184: 5 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 17.370 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 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 : 0.006 0.233 17640 Z= 0.461 Angle : 0.752 20.720 25065 Z= 0.607 Chirality : 0.045 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/Z covalent geometry : bond 0.00562 / 0.46 (17640) covalent geometry : angle 0.75174 / 0.61 (25065) hydrogen bonds : bond 0.11863 / 7.85 ( 970) hydrogen bonds : angle 8.13508 / 5.58 ( 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 : 0.487 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: 0.6457 (tp) cc_final: 0.5682 (mt) REVERT: O 770 TYR cc_start: 0.6637 (p90) cc_final: 0.6226 (p90) REVERT: O 792 ASP cc_start: 0.7165 (p0) cc_final: 0.6471 (p0) REVERT: O 809 LEU cc_start: 0.5287 (mt) cc_final: 0.4959 (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: 0.8554 (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: 0.6272 (tpp80) REVERT: O 1024 GLN cc_start: 0.7364 (mp10) cc_final: 0.6398 (tm-30) REVERT: O 1115 ILE cc_start: 0.8583 (mp) cc_final: 0.8294 (tt) REVERT: O 1132 ARG cc_start: 0.8339 (ptm-80) cc_final: 0.7855 (tmm160) REVERT: O 1140 ASP cc_start: 0.8112 (m-30) cc_final: 0.7243 (t0) REVERT: O 1160 ILE cc_start: 0.7703 (mt) cc_final: 0.7464 (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: 0.8703 (m-40) cc_final: 0.8342 (m110) REVERT: C 84 GLN cc_start: 0.7921 (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: 0.8073 (mt) cc_final: 0.7708 (mt) REVERT: E 42 ARG cc_start: 0.7541 (ttm170) cc_final: 0.7100 (tpp-160) 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: 0.7099 (mt0) REVERT: G 64 GLU cc_start: 0.7964 (tt0) cc_final: 0.7541 (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: 0.8745 (mm-40) REVERT: H 33 SER cc_start: 0.8514 (t) cc_final: 0.8264 (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: 0.1869 time to fit residues: 91.6509 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 : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 40.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 749 HIS O 787 ASN O 913 HIS O 915 HIS ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1025 GLN O1071 GLN O1104 HIS A 39 HIS A 68 GLN B 25 ASN D 79 HIS D 81 ASN E 68 GLN F 93 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.143616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.121548 restraints weight = 27162.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120120 restraints weight = 53565.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.120298 restraints weight = 49573.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120467 restraints weight = 37885.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.120446 restraints weight = 35012.798| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 17640 Z= 0.196 Angle : 0.707 10.270 25065 Z= 0.399 Chirality : 0.046 0.267 2854 Planarity : 0.006 0.150 2160 Dihedral : 28.192 172.179 4676 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.09 % Allowed : 2.53 % Favored : 97.38 % 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: -1.19 (0.22), residues: 1309 helix: -0.30 (0.18), residues: 811 sheet: -2.42 (0.54), residues: 61 loop : -1.23 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG O1316 TYR 0.024 0.002 TYR F 98 PHE 0.020 0.002 PHE O1241 TRP 0.017 0.002 TRP O1083 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 (17640) covalent geometry : angle 0.70743 / 0.40 (25065) hydrogen bonds : bond 0.05307 / 3.44 ( 970) hydrogen bonds : angle 5.31441 / 3.64 ( 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 238 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.355 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: 0.6129 (mp10) cc_final: 0.5533 (tp40) REVERT: O 1114 GLN cc_start: 0.7122 (mp10) cc_final: 0.6753 (mp10) REVERT: O 1115 ILE cc_start: 0.8084 (mp) cc_final: 0.7795 (mm) REVERT: O 1140 ASP cc_start: 0.6619 (m-30) cc_final: 0.6331 (t0) REVERT: O 1144 GLU cc_start: 0.6917 (tt0) cc_final: 0.6642 (tt0) REVERT: O 1214 THR cc_start: 0.5258 (p) cc_final: 0.4875 (p) REVERT: A 120 MET cc_start: 0.8581 (mmm) cc_final: 0.8232 (mmm) REVERT: B 74 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7287 (mt-10) REVERT: C 84 GLN cc_start: 0.8117 (tp40) cc_final: 0.7711 (tp40) REVERT: D 68 GLU cc_start: 0.7037 (tt0) cc_final: 0.6732 (tt0) REVERT: D 79 HIS cc_start: 0.7646 (OUTLIER) cc_final: 0.7193 (t-90) REVERT: D 80 TYR cc_start: 0.7130 (m-10) cc_final: 0.6884 (m-10) REVERT: E 90 MET cc_start: 0.7368 (mmm) cc_final: 0.6464 (mmt) REVERT: E 129 ARG cc_start: 0.7528 (tpt-90) cc_final: 0.6557 (tpt90) REVERT: F 72 TYR cc_start: 0.8142 (m-80) cc_final: 0.7637 (m-80) REVERT: F 91 LYS cc_start: 0.8340 (tttt) cc_final: 0.8075 (ttpp) REVERT: G 94 ASN cc_start: 0.8142 (t0) cc_final: 0.7899 (t0) REVERT: G 95 LYS cc_start: 0.7658 (tptm) cc_final: 0.7201 (mtpt) REVERT: H 33 SER cc_start: 0.8925 (t) cc_final: 0.8607 (m) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.1638 time to fit residues: 54.7397 Evaluate side-chains 164 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [129, 24, 88, 10, 86, 154, 22, 5, 84, 75, 65] chunk 129 optimal weight: 50.0000 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 154 optimal weight: 30.0000 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 681 HIS ** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 HIS D 46 HIS 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 = 0.3921 r_free = 0.3921 target = 0.144956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122019 restraints weight = 27025.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.120714 restraints weight = 50636.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120668 restraints weight = 45754.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120026 restraints weight = 39326.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120104 restraints weight = 37798.176| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17640 Z= 0.168 Angle : 0.662 8.752 25065 Z= 0.375 Chirality : 0.044 0.287 2854 Planarity : 0.005 0.054 2160 Dihedral : 28.346 173.612 4676 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: -0.50 (0.23), residues: 1309 helix: 0.32 (0.18), residues: 811 sheet: -1.75 (0.57), residues: 60 loop : -1.19 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 42 TYR 0.024 0.002 TYR O 810 PHE 0.020 0.002 PHE O1241 TRP 0.019 0.002 TRP O 777 HIS 0.007 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (17640) covalent geometry : angle 0.66181 / 0.38 (25065) hydrogen bonds : bond 0.04989 / 3.21 ( 970) hydrogen bonds : angle 4.77085 / 3.27 ( 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 218 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 850 SER cc_start: 0.7403 (p) cc_final: 0.6443 (p) REVERT: O 943 PRO cc_start: 0.2329 (Cg_exo) cc_final: 0.2128 (Cg_endo) REVERT: O 1024 GLN cc_start: 0.6089 (mp10) cc_final: 0.5441 (tp40) REVERT: O 1115 ILE cc_start: 0.8232 (mp) cc_final: 0.7671 (mp) REVERT: O 1140 ASP cc_start: 0.6843 (m-30) cc_final: 0.6433 (t0) REVERT: O 1144 GLU cc_start: 0.6862 (tt0) cc_final: 0.6621 (tt0) REVERT: B 74 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7370 (mt-10) REVERT: D 85 THR cc_start: 0.9181 (m) cc_final: 0.8831 (t) REVERT: E 79 LYS cc_start: 0.8084 (tttp) cc_final: 0.7830 (tttm) REVERT: E 90 MET cc_start: 0.7341 (mmm) cc_final: 0.6753 (mmt) REVERT: E 129 ARG cc_start: 0.7453 (tpt-90) cc_final: 0.6493 (tpt90) REVERT: F 72 TYR cc_start: 0.8039 (m-80) cc_final: 0.7823 (m-80) REVERT: G 94 ASN cc_start: 0.8132 (t0) cc_final: 0.7873 (t0) REVERT: G 95 LYS cc_start: 0.7509 (tptm) cc_final: 0.7197 (mtpt) REVERT: H 33 SER cc_start: 0.8881 (t) cc_final: 0.8547 (m) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1396 time to fit residues: 44.3325 Evaluate side-chains 163 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [130, 3, 51, 135, 20, 11, 55, 63, 153, 84, 52] chunk 130 optimal weight: 40.0000 chunk 3 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 135 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 787 ASN ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN O1237 GLN A 39 HIS D 81 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.140757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.117493 restraints weight = 27214.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.116527 restraints weight = 57248.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.116733 restraints weight = 53203.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116122 restraints weight = 43145.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116218 restraints weight = 44912.611| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 17640 Z= 0.247 Angle : 0.734 8.808 25065 Z= 0.404 Chirality : 0.047 0.309 2854 Planarity : 0.005 0.055 2160 Dihedral : 28.670 174.567 4676 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: -0.50 (0.22), residues: 1309 helix: 0.34 (0.18), residues: 809 sheet: -1.73 (0.59), residues: 60 loop : -1.25 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 76 TYR 0.027 0.002 TYR O 810 PHE 0.021 0.002 PHE O1159 TRP 0.018 0.002 TRP O 777 HIS 0.009 0.002 HIS O 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 (17640) covalent geometry : angle 0.73427 / 0.40 (25065) hydrogen bonds : bond 0.05705 / 3.69 ( 970) hydrogen bonds : angle 4.70634 / 3.22 ( 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 202 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1024 GLN cc_start: 0.6568 (mp10) cc_final: 0.5764 (tp40) REVERT: C 75 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7210 (mtmt) REVERT: E 79 LYS cc_start: 0.7630 (tttp) cc_final: 0.7402 (tttm) REVERT: E 129 ARG cc_start: 0.7517 (tpt-90) cc_final: 0.6532 (tpt90) REVERT: G 95 LYS cc_start: 0.7530 (tptm) cc_final: 0.7254 (mtpt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1366 time to fit residues: 40.7049 Evaluate side-chains 151 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [19, 34, 133, 154, 20, 99, 91, 51, 86, 52, 68] chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 133 optimal weight: 30.0000 chunk 154 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 30.0000 chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1237 GLN A 39 HIS D 81 ASN F 75 HIS F 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.143012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120240 restraints weight = 26764.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.118971 restraints weight = 53994.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.119242 restraints weight = 47084.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119001 restraints weight = 37446.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.119155 restraints weight = 36815.591| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17640 Z= 0.161 Angle : 0.653 8.333 25065 Z= 0.368 Chirality : 0.043 0.303 2854 Planarity : 0.005 0.052 2160 Dihedral : 28.546 175.222 4676 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: 0.77 (0.18), residues: 814 sheet: -1.68 (0.63), residues: 61 loop : -1.08 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG G 29 TYR 0.022 0.002 TYR O 810 PHE 0.015 0.002 PHE O1159 TRP 0.017 0.001 TRP O 777 HIS 0.011 0.001 HIS O 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (17640) covalent geometry : angle 0.65340 / 0.37 (25065) hydrogen bonds : bond 0.04914 / 3.17 ( 970) hydrogen bonds : angle 4.41548 / 3.02 ( 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 217 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1024 GLN cc_start: 0.6569 (mp10) cc_final: 0.5747 (tp40) REVERT: D 80 TYR cc_start: 0.7175 (m-10) cc_final: 0.6926 (m-10) REVERT: E 129 ARG cc_start: 0.7457 (tpt-90) cc_final: 0.6431 (tpt90) REVERT: F 72 TYR cc_start: 0.7964 (m-80) cc_final: 0.7383 (m-80) REVERT: G 75 LYS cc_start: 0.7067 (mmtt) cc_final: 0.6814 (mtmt) REVERT: G 95 LYS cc_start: 0.7573 (tptm) cc_final: 0.7278 (mtpt) REVERT: H 85 THR cc_start: 0.9165 (t) cc_final: 0.8889 (p) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1312 time to fit residues: 42.6622 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 : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [92, 26, 97, 115, 101, 104, 154, 42, 65, 114, 89] chunk 92 optimal weight: 8.9990 chunk 26 optimal weight: 0.0370 chunk 97 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 154 optimal weight: 30.0000 chunk 42 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1079 ASN O1171 ASN O1237 GLN A 39 HIS D 81 ASN F 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.143268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.119010 restraints weight = 26895.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.118117 restraints weight = 54947.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.118418 restraints weight = 51322.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118093 restraints weight = 45030.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118210 restraints weight = 46051.770| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17640 Z= 0.153 Angle : 0.631 8.632 25065 Z= 0.357 Chirality : 0.043 0.313 2854 Planarity : 0.004 0.052 2160 Dihedral : 28.501 176.826 4676 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.65 % 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: 0.33 (0.23), residues: 1309 helix: 1.03 (0.19), residues: 819 sheet: -1.47 (0.64), residues: 61 loop : -1.02 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 96 TYR 0.022 0.002 TYR O 810 PHE 0.014 0.002 PHE O1159 TRP 0.022 0.001 TRP O 777 HIS 0.007 0.001 HIS O 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (17640) covalent geometry : angle 0.63141 / 0.36 (25065) hydrogen bonds : bond 0.04713 / 3.05 ( 970) hydrogen bonds : angle 4.25753 / 2.91 ( 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 209 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 855 LYS cc_start: 0.8388 (mmmt) cc_final: 0.7939 (mmtt) REVERT: O 1022 MET cc_start: 0.7066 (mmm) cc_final: 0.6405 (tpp) REVERT: O 1024 GLN cc_start: 0.6449 (mp10) cc_final: 0.5951 (tp40) REVERT: O 1150 ASN cc_start: 0.7561 (m110) cc_final: 0.6641 (t0) REVERT: O 1349 ARG cc_start: 0.2089 (mmt-90) cc_final: 0.1424 (ptm160) REVERT: B 27 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7270 (mp10) REVERT: C 77 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7403 (ttm-80) REVERT: D 80 TYR cc_start: 0.7087 (m-10) cc_final: 0.6796 (m-10) REVERT: D 119 THR cc_start: 0.8072 (t) cc_final: 0.7862 (m) REVERT: E 129 ARG cc_start: 0.7438 (tpt-90) cc_final: 0.6604 (tpt90) REVERT: F 72 TYR cc_start: 0.8001 (m-80) cc_final: 0.7455 (m-80) REVERT: G 75 LYS cc_start: 0.7093 (mmtt) cc_final: 0.6777 (mtmt) REVERT: G 95 LYS cc_start: 0.7582 (tptm) cc_final: 0.7262 (mtpt) REVERT: H 56 MET cc_start: 0.8312 (tpp) cc_final: 0.8089 (tpp) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1402 time to fit residues: 42.4418 Evaluate side-chains 154 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [55, 112, 100, 3, 89, 128, 131, 49, 142, 132, 13] chunk 55 optimal weight: 0.0040 chunk 112 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 131 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 chunk 142 optimal weight: 50.0000 chunk 132 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 overall best weight: 4.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN O1171 ASN ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1237 GLN A 39 HIS ** D 81 ASN ** 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 = 0.3874 r_free = 0.3874 target = 0.140991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.118405 restraints weight = 27076.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.117380 restraints weight = 55008.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.117797 restraints weight = 53761.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.117385 restraints weight = 40226.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117731 restraints weight = 40812.352| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3686 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= 0.209 Angle : 0.695 8.633 25065 Z= 0.385 Chirality : 0.045 0.325 2854 Planarity : 0.005 0.050 2160 Dihedral : 28.656 178.323 4676 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.81 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: 0.85 (0.18), residues: 827 sheet: -1.59 (0.65), residues: 61 loop : -1.14 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 71 TYR 0.026 0.002 TYR O 810 PHE 0.023 0.002 PHE O1159 TRP 0.021 0.002 TRP O 777 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (17640) covalent geometry : angle 0.69534 / 0.38 (25065) hydrogen bonds : bond 0.05269 / 3.40 ( 970) hydrogen bonds : angle 4.32819 / 2.95 ( 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 201 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 1022 MET cc_start: 0.7047 (mmm) cc_final: 0.6407 (tpp) REVERT: O 1024 GLN cc_start: 0.6363 (mp10) cc_final: 0.6050 (tp40) REVERT: O 1150 ASN cc_start: 0.7538 (m110) cc_final: 0.6613 (t0) REVERT: O 1214 THR cc_start: 0.5158 (p) cc_final: 0.4954 (p) REVERT: O 1349 ARG cc_start: 0.2255 (mmt-90) cc_final: 0.1329 (ptm160) REVERT: B 92 ARG cc_start: 0.7961 (tpt-90) cc_final: 0.7733 (ttt90) REVERT: C 38 ASN cc_start: 0.7986 (m-40) cc_final: 0.7603 (p0) REVERT: C 75 LYS cc_start: 0.7827 (mmtt) cc_final: 0.7495 (mtmt) REVERT: D 39 TYR cc_start: 0.7817 (t80) cc_final: 0.7460 (t80) REVERT: D 80 TYR cc_start: 0.7090 (m-10) cc_final: 0.6825 (m-10) REVERT: E 129 ARG cc_start: 0.7568 (tpt-90) cc_final: 0.6601 (tpt90) REVERT: G 95 LYS cc_start: 0.7485 (tptm) cc_final: 0.7270 (mtpt) REVERT: H 102 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7464 (mm-30) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1310 time to fit residues: 39.2524 Evaluate side-chains 160 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [19, 93, 115, 136, 65, 71, 40, 85, 62, 126, 123] chunk 19 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 136 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1171 ASN O1237 GLN A 39 HIS B 75 HIS D 81 ASN G 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.144456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.122581 restraints weight = 27101.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.121815 restraints weight = 44203.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.121776 restraints weight = 48495.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121007 restraints weight = 39223.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121171 restraints weight = 41447.995| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17640 Z= 0.134 Angle : 0.612 8.457 25065 Z= 0.351 Chirality : 0.042 0.319 2854 Planarity : 0.004 0.050 2160 Dihedral : 28.427 179.186 4676 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.90 % Favored : 95.95 % Rotamer: Outliers : 0.09 % Allowed : 1.05 % Favored : 98.86 % 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: 0.58 (0.23), residues: 1309 helix: 1.27 (0.19), residues: 829 sheet: -1.38 (0.65), residues: 61 loop : -1.07 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 76 TYR 0.018 0.002 TYR O 810 PHE 0.014 0.002 PHE O1159 TRP 0.026 0.001 TRP O 777 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.13 (17640) covalent geometry : angle 0.61225 / 0.35 (25065) hydrogen bonds : bond 0.04421 / 2.84 ( 970) hydrogen bonds : angle 4.02698 / 2.75 ( 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 209 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1022 MET cc_start: 0.7023 (mmm) cc_final: 0.6435 (tpp) REVERT: O 1024 GLN cc_start: 0.6407 (mp10) cc_final: 0.5964 (tp40) REVERT: O 1140 ASP cc_start: 0.7005 (m-30) cc_final: 0.6605 (t0) REVERT: O 1150 ASN cc_start: 0.7398 (m110) cc_final: 0.6628 (t0) REVERT: O 1349 ARG cc_start: 0.2076 (mmt-90) cc_final: 0.1417 (ptm160) REVERT: B 27 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7511 (mp10) REVERT: C 75 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7433 (mtmt) REVERT: D 39 TYR cc_start: 0.7596 (t80) cc_final: 0.7255 (t80) REVERT: E 129 ARG cc_start: 0.7482 (tpt-90) cc_final: 0.6599 (tpt90) REVERT: F 74 GLU cc_start: 0.6516 (mm-30) cc_final: 0.6308 (mm-30) REVERT: G 73 ASN cc_start: 0.6968 (OUTLIER) cc_final: 0.6677 (t160) REVERT: G 95 LYS cc_start: 0.7588 (tptm) cc_final: 0.7240 (mtpt) REVERT: H 76 ARG cc_start: 0.6117 (mtm-85) cc_final: 0.5769 (mtp85) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1364 time to fit residues: 42.2169 Evaluate side-chains 160 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [58, 59, 108, 119, 137, 27, 60, 87, 38, 68, 97] chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 137 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 60 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1171 ASN O1237 GLN A 39 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.144105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121182 restraints weight = 27009.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.120033 restraints weight = 48885.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119639 restraints weight = 51417.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119129 restraints weight = 42095.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119159 restraints weight = 39479.190| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17640 Z= 0.136 Angle : 0.623 11.285 25065 Z= 0.352 Chirality : 0.042 0.327 2854 Planarity : 0.004 0.049 2160 Dihedral : 28.437 179.584 4676 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.51 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 0.67 (0.23), residues: 1309 helix: 1.39 (0.19), residues: 825 sheet: -1.42 (0.65), residues: 61 loop : -1.12 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG O1132 TYR 0.021 0.001 TYR O 810 PHE 0.016 0.002 PHE O1159 TRP 0.028 0.002 TRP O 777 HIS 0.010 0.001 HIS O 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (17640) covalent geometry : angle 0.62270 / 0.35 (25065) hydrogen bonds : bond 0.04405 / 2.85 ( 970) hydrogen bonds : angle 3.99419 / 2.73 ( 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 201 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1022 MET cc_start: 0.6833 (mmm) cc_final: 0.6384 (tpp) REVERT: O 1024 GLN cc_start: 0.6527 (mp10) cc_final: 0.6023 (tp40) REVERT: O 1140 ASP cc_start: 0.7012 (m-30) cc_final: 0.6562 (t0) REVERT: O 1150 ASN cc_start: 0.7426 (m110) cc_final: 0.6672 (t0) REVERT: O 1214 THR cc_start: 0.5057 (p) cc_final: 0.4847 (p) REVERT: O 1349 ARG cc_start: 0.2009 (mmt-90) cc_final: 0.1388 (ptm160) REVERT: A 115 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7809 (mmmm) REVERT: B 27 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7284 (mp10) REVERT: B 92 ARG cc_start: 0.8294 (ttt90) cc_final: 0.8091 (ttt180) REVERT: C 75 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7399 (mtmt) REVERT: C 108 LEU cc_start: 0.8304 (mt) cc_final: 0.8089 (mt) REVERT: D 82 LYS cc_start: 0.8525 (mttm) cc_final: 0.8252 (mttm) REVERT: E 90 MET cc_start: 0.7057 (mmt) cc_final: 0.6683 (mmt) REVERT: E 129 ARG cc_start: 0.7395 (tpt-90) cc_final: 0.6589 (tpt90) REVERT: G 95 LYS cc_start: 0.7496 (tptm) cc_final: 0.7170 (mtpt) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1359 time to fit residues: 40.7612 Evaluate side-chains 160 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [116, 132, 38, 25, 98, 112, 73, 7, 82, 150, 44] chunk 116 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 150 optimal weight: 30.0000 chunk 44 optimal weight: 0.1980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN O1171 ASN O1237 GLN A 39 HIS F 18 HIS F 25 ASN F 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.143191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.118844 restraints weight = 27013.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117688 restraints weight = 63605.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.117776 restraints weight = 54198.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117685 restraints weight = 42723.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.117797 restraints weight = 38837.803| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17640 Z= 0.153 Angle : 0.630 9.527 25065 Z= 0.355 Chirality : 0.042 0.331 2854 Planarity : 0.004 0.050 2160 Dihedral : 28.491 178.798 4676 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.35 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.61 (0.23), residues: 1309 helix: 1.34 (0.19), residues: 831 sheet: -1.39 (0.65), residues: 61 loop : -1.19 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O1132 TYR 0.024 0.002 TYR H 80 PHE 0.018 0.002 PHE O1159 TRP 0.027 0.002 TRP O 777 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (17640) covalent geometry : angle 0.63005 / 0.35 (25065) hydrogen bonds : bond 0.04541 / 2.94 ( 970) hydrogen bonds : angle 3.98411 / 2.72 ( 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 195 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1140 ASP cc_start: 0.7043 (m-30) cc_final: 0.6632 (t0) REVERT: O 1150 ASN cc_start: 0.7554 (m110) cc_final: 0.6686 (t0) REVERT: O 1214 THR cc_start: 0.5045 (p) cc_final: 0.4837 (p) REVERT: O 1349 ARG cc_start: 0.2052 (mmt-90) cc_final: 0.1383 (ptm160) REVERT: B 27 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7060 (mp10) REVERT: C 75 LYS cc_start: 0.7809 (mmtt) cc_final: 0.7493 (mtmt) REVERT: D 82 LYS cc_start: 0.8514 (mttm) cc_final: 0.8241 (mttm) REVERT: E 90 MET cc_start: 0.7139 (mmt) cc_final: 0.6811 (mmt) REVERT: E 129 ARG cc_start: 0.7401 (tpt-90) cc_final: 0.6584 (tpt90) REVERT: G 95 LYS cc_start: 0.7544 (tptm) cc_final: 0.7210 (mtpt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1293 time to fit residues: 37.9931 Evaluate side-chains 161 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [56, 65, 43, 46, 11, 21, 84, 74, 102, 155, 103] chunk 56 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 chunk 103 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN O1171 ASN A 39 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 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 = 0.3884 r_free = 0.3884 target = 0.141627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.118919 restraints weight = 27195.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.117526 restraints weight = 50854.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116543 restraints weight = 57519.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115860 restraints weight = 47597.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115376 restraints weight = 50834.527| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17640 Z= 0.187 Angle : 0.677 11.755 25065 Z= 0.375 Chirality : 0.044 0.341 2854 Planarity : 0.005 0.051 2160 Dihedral : 28.607 178.212 4676 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.97 % Favored : 94.88 % 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: 0.39 (0.23), residues: 1309 helix: 1.19 (0.19), residues: 824 sheet: -1.58 (0.62), residues: 61 loop : -1.25 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 92 TYR 0.033 0.002 TYR H 80 PHE 0.021 0.002 PHE O1159 TRP 0.025 0.002 TRP O 777 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (17640) covalent geometry : angle 0.67736 / 0.38 (25065) hydrogen bonds : bond 0.04989 / 3.23 ( 970) hydrogen bonds : angle 4.11193 / 2.80 ( 2517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2066.27 seconds wall clock time: 36 minutes 36.85 seconds (2196.85 seconds total)