Starting phenix.real_space_refine on Sat Sep 12 18:11:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cvo_27011/09_2026/8cvo_27011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cvo_27011/09_2026/8cvo_27011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8cvo_27011/09_2026/8cvo_27011.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cvo_27011/09_2026/8cvo_27011.cif" model { file = "/net/cci-nas-00/data/ceres_data/8cvo_27011/09_2026/8cvo_27011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cvo_27011/09_2026/8cvo_27011.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cvo_27011/09_2026/8cvo_27011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cvo_27011/09_2026/8cvo_27011.map" } resolution = 2.95 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= 0.000 sd= 0.031 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 471 5.49 5 Mg 12 5.21 5 S 23 5.16 5 C 9071 2.51 5 N 3239 2.21 5 O 4604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17421 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 10090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 10090 Classifications: {'RNA': 2, 'RNAv2': 469} Modifications used: {'rna2p_pur': 34, 'rna2p_pyr': 37, 'rna3p': 2, 'rna3p_pur': 219, 'rna3p_pyr': 179} Link IDs: {'rna2p': 71, 'rna3p': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "E" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 482 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "G" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1670 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 209} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1225 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "J" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1012 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 125} Chain: "M" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 90} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "S" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 474 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "U" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 658 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 47 Unusual residues: {' MG': 12, 'V7A': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16420 SG CYS S 24 47.536 67.044 47.555 1.00 68.29 S ATOM 16446 SG CYS S 27 46.769 63.105 48.246 1.00 69.39 S ATOM 16552 SG CYS S 40 50.103 65.280 49.667 1.00 69.26 S ATOM 16577 SG CYS S 43 49.456 64.842 46.134 1.00 70.06 S Time building chain proxies: 3.50, per 1000 atoms: 0.20 Number of scatterers: 17421 At special positions: 0 Unit cell: (129.228, 129.228, 124.956, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 23 16.00 P 471 15.00 Mg 12 11.99 O 4604 8.00 N 3239 7.00 C 9071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 426.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S 101 " pdb="ZN ZN S 101 " - pdb=" SG CYS S 43 " pdb="ZN ZN S 101 " - pdb=" SG CYS S 40 " pdb="ZN ZN S 101 " - pdb=" SG CYS S 24 " pdb="ZN ZN S 101 " - pdb=" SG CYS S 27 " Number of angles added : 6 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 8 sheets defined 45.8% alpha, 21.4% beta 140 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'E' and resid 78 through 92 removed outlier: 4.174A pdb=" N LYS E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 11 Processing helix chain 'G' and resid 27 through 46 Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 80 through 95 Processing helix chain 'G' and resid 111 through 125 Processing helix chain 'G' and resid 128 through 144 Processing helix chain 'G' and resid 155 through 159 removed outlier: 3.518A pdb=" N ALA G 159 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 215 Processing helix chain 'I' and resid 20 through 31 removed outlier: 3.741A pdb=" N SER I 24 " --> pdb=" O SER I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 34 No H-bonds generated for 'chain 'I' and resid 32 through 34' Processing helix chain 'I' and resid 35 through 54 Processing helix chain 'I' and resid 57 through 70 Processing helix chain 'I' and resid 92 through 111 Processing helix chain 'I' and resid 115 through 130 Processing helix chain 'I' and resid 132 through 148 Processing helix chain 'I' and resid 149 through 155 removed outlier: 4.752A pdb=" N HIS I 153 " --> pdb=" O ALA I 150 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG I 155 " --> pdb=" O ALA I 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 81 Processing helix chain 'J' and resid 87 through 97 Proline residue: J 93 - end of helix Processing helix chain 'J' and resid 113 through 133 Processing helix chain 'J' and resid 137 through 144 Processing helix chain 'M' and resid 14 through 32 Processing helix chain 'M' and resid 80 through 90 Processing helix chain 'N' and resid 14 through 19 Processing helix chain 'N' and resid 26 through 38 Processing helix chain 'N' and resid 49 through 64 Processing helix chain 'N' and resid 67 through 85 Processing helix chain 'N' and resid 86 through 95 Processing helix chain 'N' and resid 107 through 112 Processing helix chain 'S' and resid 3 through 12 Processing helix chain 'S' and resid 16 through 20 Processing helix chain 'S' and resid 40 through 51 Processing helix chain 'U' and resid 4 through 8 Processing helix chain 'U' and resid 14 through 26 Processing helix chain 'U' and resid 41 through 45 Processing helix chain 'U' and resid 63 through 69 removed outlier: 3.727A pdb=" N VAL U 67 " --> pdb=" O GLU U 64 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY U 68 " --> pdb=" O SER U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 75 Processing sheet with id=AA1, first strand: chain 'E' and resid 35 through 47 removed outlier: 5.218A pdb=" N GLU E 36 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLY E 63 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL E 38 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL E 61 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA E 40 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 20 through 21 removed outlier: 3.627A pdb=" N ARG G 58 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR G 68 " --> pdb=" O SER G 52 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE G 54 " --> pdb=" O PHE G 66 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE G 66 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE G 56 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR G 64 " --> pdb=" O ILE G 56 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG G 58 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL G 63 " --> pdb=" O GLN G 99 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASN G 101 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE G 65 " --> pdb=" O ASN G 101 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU G 103 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU G 67 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 163 through 170 removed outlier: 3.731A pdb=" N GLY G 147 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASP G 180 " --> pdb=" O LYS G 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 73 through 78 Processing sheet with id=AA5, first strand: chain 'J' and resid 48 through 53 removed outlier: 6.529A pdb=" N LYS J 71 " --> pdb=" O ALA J 107 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE J 109 " --> pdb=" O LYS J 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 36 through 52 removed outlier: 8.548A pdb=" N ASP M 75 " --> pdb=" O PRO M 39 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU M 73 " --> pdb=" O PRO M 41 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS M 71 " --> pdb=" O PRO M 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN M 47 " --> pdb=" O MET M 67 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG M 11 " --> pdb=" O ASP M 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 36 through 52 removed outlier: 8.548A pdb=" N ASP M 75 " --> pdb=" O PRO M 39 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU M 73 " --> pdb=" O PRO M 41 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS M 71 " --> pdb=" O PRO M 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN M 47 " --> pdb=" O MET M 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'U' and resid 30 through 33 372 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 353 hydrogen bonds 530 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 4.15 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2732 1.33 - 1.45: 7103 1.45 - 1.57: 7908 1.57 - 1.69: 941 1.69 - 1.81: 39 Bond restraints: 18723 Sorted by residual: bond pdb=" CBC V7A A1601 " pdb=" NBD V7A A1601 " ideal model delta sigma weight residual 1.323 1.509 -0.186 2.00e-02 2.50e+03 8.67e+01 bond pdb=" N VAL M 36 " pdb=" CA VAL M 36 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.89e+00 bond pdb=" N VAL G 206 " pdb=" CA VAL G 206 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.15e-02 7.56e+03 7.84e+00 bond pdb=" N GLU G 25 " pdb=" CA GLU G 25 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.14e-02 7.69e+03 7.58e+00 bond pdb=" N LYS M 35 " pdb=" CA LYS M 35 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.33e+00 ... (remaining 18718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 26422 2.65 - 5.30: 1116 5.30 - 7.95: 47 7.95 - 10.60: 9 10.60 - 13.25: 2 Bond angle restraints: 27596 Sorted by residual: angle pdb=" C3' G A1184 " pdb=" O3' G A1184 " pdb=" P U A1185 " ideal model delta sigma weight residual 119.70 106.45 13.25 1.20e+00 6.94e-01 1.22e+02 angle pdb=" C3' U A1153 " pdb=" O3' U A1153 " pdb=" P C A1154 " ideal model delta sigma weight residual 119.70 108.99 10.71 1.20e+00 6.94e-01 7.96e+01 angle pdb=" C3' U A 958 " pdb=" O3' U A 958 " pdb=" P A A 959 " ideal model delta sigma weight residual 119.70 109.13 10.57 1.20e+00 6.94e-01 7.75e+01 angle pdb=" C3' A A1343 " pdb=" O3' A A1343 " pdb=" P U A1344 " ideal model delta sigma weight residual 119.70 109.89 9.81 1.20e+00 6.94e-01 6.68e+01 angle pdb=" C3' A A 959 " pdb=" O3' A A 959 " pdb=" P G A 960 " ideal model delta sigma weight residual 119.70 110.11 9.59 1.20e+00 6.94e-01 6.38e+01 ... (remaining 27591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 9364 34.98 - 69.96: 816 69.96 - 104.94: 75 104.94 - 139.92: 1 139.92 - 174.90: 4 Dihedral angle restraints: 10260 sinusoidal: 7616 harmonic: 2644 Sorted by residual: dihedral pdb=" C4' G A1038 " pdb=" C3' G A1038 " pdb=" C2' G A1038 " pdb=" C1' G A1038 " ideal model delta sinusoidal sigma weight residual 36.34 -44.28 80.63 1 3.10e+00 1.04e-01 8.36e+02 dihedral pdb=" C4' U A 958 " pdb=" C3' U A 958 " pdb=" C2' U A 958 " pdb=" C1' U A 958 " ideal model delta sinusoidal sigma weight residual 36.34 -43.72 80.07 1 3.10e+00 1.04e-01 8.27e+02 dihedral pdb=" C4' G A 960 " pdb=" C3' G A 960 " pdb=" C2' G A 960 " pdb=" C1' G A 960 " ideal model delta sinusoidal sigma weight residual 36.35 -42.77 79.12 1 3.10e+00 1.04e-01 8.10e+02 ... (remaining 10257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2822 0.132 - 0.265: 528 0.265 - 0.397: 86 0.397 - 0.529: 0 0.529 - 0.662: 18 Chirality restraints: 3454 Sorted by residual: chirality pdb=" P G A1184 " pdb=" OP1 G A1184 " pdb=" OP2 G A1184 " pdb=" O5' G A1184 " both_signs ideal model delta sigma weight residual True 2.17 -2.83 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" P U A1153 " pdb=" OP1 U A1153 " pdb=" OP2 U A1153 " pdb=" O5' U A1153 " both_signs ideal model delta sigma weight residual True 2.17 -2.83 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P U A 958 " pdb=" OP1 U A 958 " pdb=" OP2 U A 958 " pdb=" O5' U A 958 " both_signs ideal model delta sigma weight residual True 2.17 -2.82 -0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 3451 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAH V7A A1601 " 0.298 2.00e-02 2.50e+03 2.47e-01 9.13e+02 pdb=" CAI V7A A1601 " 0.005 2.00e-02 2.50e+03 pdb=" CAJ V7A A1601 " -0.293 2.00e-02 2.50e+03 pdb=" CAL V7A A1601 " -0.018 2.00e-02 2.50e+03 pdb=" CAM V7A A1601 " 0.313 2.00e-02 2.50e+03 pdb=" OAZ V7A A1601 " -0.304 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A1039 " -0.045 2.00e-02 2.50e+03 4.06e-02 3.70e+01 pdb=" N1 C A1039 " 0.027 2.00e-02 2.50e+03 pdb=" C2 C A1039 " 0.088 2.00e-02 2.50e+03 pdb=" O2 C A1039 " -0.010 2.00e-02 2.50e+03 pdb=" N3 C A1039 " -0.053 2.00e-02 2.50e+03 pdb=" C4 C A1039 " -0.023 2.00e-02 2.50e+03 pdb=" N4 C A1039 " -0.001 2.00e-02 2.50e+03 pdb=" C5 C A1039 " 0.027 2.00e-02 2.50e+03 pdb=" C6 C A1039 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP M 27 " 0.014 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C ASP M 27 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP M 27 " 0.019 2.00e-02 2.50e+03 pdb=" N THR M 28 " 0.017 2.00e-02 2.50e+03 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 525 2.64 - 3.20: 15170 3.20 - 3.77: 34652 3.77 - 4.33: 46716 4.33 - 4.90: 63682 Nonbonded interactions: 160745 Sorted by model distance: nonbonded pdb=" OP2 G A1184 " pdb="MG MG A1604 " model vdw 2.075 2.170 nonbonded pdb=" OP2 A A1095 " pdb="MG MG A1612 " model vdw 2.211 2.170 nonbonded pdb=" O VAL J 85 " pdb=" NE2 GLN J 88 " model vdw 2.223 3.120 nonbonded pdb=" N2 G A1163 " pdb=" O6 G A1167 " model vdw 2.226 3.120 nonbonded pdb=" OP2 U A 945 " pdb=" O2' C A1209 " model vdw 2.241 3.040 ... (remaining 160740 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.560 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 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 : 0.005 0.186 18727 Z= 0.252 Angle : 0.974 21.698 27602 Z= 0.447 Chirality : 0.112 0.662 3454 Planarity : 0.008 0.247 1764 Dihedral : 19.922 174.901 8562 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.77 % Allowed : 5.57 % Favored : 93.66 % Rotamer: Outliers : 1.47 % Allowed : 0.53 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.29), residues: 915 helix: 1.21 (0.28), residues: 367 sheet: -0.15 (0.39), residues: 173 loop : -0.81 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 93 TYR 0.024 0.002 TYR N 64 PHE 0.018 0.002 PHE S 37 TRP 0.008 0.001 TRP G 22 HIS 0.004 0.001 HIS J 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.25 (18723) covalent geometry : angle 0.95840 / 0.45 (27596) hydrogen bonds : bond 0.18280 / 9.40 ( 718) hydrogen bonds : angle 6.51194 / 2.53 ( 1586) metal coordination : bond 0.05865 / 2.93 ( 4) metal coordination : angle 11.91809 / 3.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 284 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7211 (m-80) cc_final: 0.6856 (m-80) REVERT: E 78 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7794 (mt-10) REVERT: E 85 LYS cc_start: 0.8832 (ttmt) cc_final: 0.8197 (ttpt) REVERT: G 161 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7940 (mmm) REVERT: I 123 GLU cc_start: 0.9045 (tp30) cc_final: 0.8834 (mm-30) REVERT: J 79 ASP cc_start: 0.9016 (t0) cc_final: 0.8655 (t0) REVERT: J 80 TYR cc_start: 0.9076 (t80) cc_final: 0.8755 (t80) REVERT: M 20 SER cc_start: 0.9191 (p) cc_final: 0.8970 (p) REVERT: M 46 LYS cc_start: 0.8416 (tptm) cc_final: 0.8163 (tppp) REVERT: M 76 ILE cc_start: 0.8874 (mm) cc_final: 0.8551 (mm) REVERT: S 46 GLU cc_start: 0.8188 (pt0) cc_final: 0.7963 (pt0) outliers start: 11 outliers final: 3 residues processed: 290 average time/residue: 0.6450 time to fit residues: 207.4375 Evaluate side-chains 219 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 215 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 66 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 27 GLN G 97 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 HIS M 47 ASN N 52 GLN ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.099152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.073400 restraints weight = 39520.597| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.65 r_work: 0.2898 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18727 Z= 0.214 Angle : 1.306 21.303 27602 Z= 0.522 Chirality : 0.116 1.075 3454 Planarity : 0.005 0.042 1764 Dihedral : 18.055 171.366 6754 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.46 % Favored : 93.88 % Rotamer: Outliers : 3.48 % Allowed : 18.18 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.29), residues: 915 helix: 1.25 (0.28), residues: 373 sheet: -0.05 (0.40), residues: 178 loop : -0.73 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 48 TYR 0.012 0.001 TYR N 64 PHE 0.012 0.001 PHE U 74 TRP 0.008 0.001 TRP G 22 HIS 0.006 0.001 HIS N 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 (18723) covalent geometry : angle 1.30434 / 0.52 (27596) hydrogen bonds : bond 0.07352 / 3.83 ( 718) hydrogen bonds : angle 3.80794 / 1.53 ( 1586) metal coordination : bond 0.00641 / 0.32 ( 4) metal coordination : angle 5.06699 / 1.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7142 (m-80) cc_final: 0.6667 (m-80) REVERT: E 78 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8436 (mt-10) REVERT: E 85 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8201 (ttpt) REVERT: E 89 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: G 17 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8292 (m-30) REVERT: G 138 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8284 (tp40) REVERT: I 41 ASN cc_start: 0.8993 (t0) cc_final: 0.8780 (t0) REVERT: I 74 GLU cc_start: 0.8371 (pp20) cc_final: 0.7995 (pp20) REVERT: I 123 GLU cc_start: 0.9273 (tp30) cc_final: 0.8935 (mm-30) REVERT: J 79 ASP cc_start: 0.9271 (t0) cc_final: 0.8759 (t0) REVERT: J 80 TYR cc_start: 0.9170 (t80) cc_final: 0.8860 (t80) REVERT: J 92 GLU cc_start: 0.8474 (pp20) cc_final: 0.8218 (pp20) REVERT: M 20 SER cc_start: 0.9164 (p) cc_final: 0.8899 (p) REVERT: M 68 ARG cc_start: 0.9012 (mtp85) cc_final: 0.8806 (mtp85) REVERT: M 76 ILE cc_start: 0.8789 (mm) cc_final: 0.8582 (mm) REVERT: N 32 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8320 (tm-30) REVERT: N 58 ASP cc_start: 0.8465 (p0) cc_final: 0.8249 (p0) outliers start: 26 outliers final: 13 residues processed: 245 average time/residue: 0.5837 time to fit residues: 159.9237 Evaluate side-chains 228 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain U residue 39 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 61 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 86 HIS N 59 HIS S 31 HIS ** U 23 ASN ** 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 = 0.3485 r_free = 0.3485 target = 0.098464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.072881 restraints weight = 39631.174| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.56 r_work: 0.2869 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18727 Z= 0.247 Angle : 1.147 14.980 27602 Z= 0.465 Chirality : 0.096 0.864 3454 Planarity : 0.005 0.044 1764 Dihedral : 18.159 179.215 6746 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.57 % Favored : 93.77 % Rotamer: Outliers : 5.48 % Allowed : 20.72 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.29), residues: 915 helix: 1.32 (0.28), residues: 374 sheet: 0.02 (0.39), residues: 182 loop : -0.71 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 48 TYR 0.014 0.002 TYR N 64 PHE 0.014 0.001 PHE U 74 TRP 0.009 0.001 TRP G 22 HIS 0.006 0.001 HIS N 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.25 (18723) covalent geometry : angle 1.14448 / 0.46 (27596) hydrogen bonds : bond 0.06306 / 3.27 ( 718) hydrogen bonds : angle 3.67381 / 1.47 ( 1586) metal coordination : bond 0.00732 / 0.37 ( 4) metal coordination : angle 5.08789 / 1.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7424 (m-80) cc_final: 0.7050 (m-80) REVERT: E 85 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8164 (ttpt) REVERT: G 48 ARG cc_start: 0.8693 (mtp85) cc_final: 0.8483 (mtp85) REVERT: G 138 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8462 (tp40) REVERT: G 141 MET cc_start: 0.9210 (mmt) cc_final: 0.8915 (mmt) REVERT: G 142 ASN cc_start: 0.8852 (m-40) cc_final: 0.8372 (m-40) REVERT: I 74 GLU cc_start: 0.8452 (pp20) cc_final: 0.8161 (pp20) REVERT: I 149 ARG cc_start: 0.7600 (tmm-80) cc_final: 0.7377 (tmm-80) REVERT: J 79 ASP cc_start: 0.9292 (t0) cc_final: 0.8771 (t0) REVERT: J 92 GLU cc_start: 0.8533 (pp20) cc_final: 0.8317 (pp20) REVERT: J 106 ILE cc_start: 0.9369 (mt) cc_final: 0.9156 (mp) REVERT: M 5 LYS cc_start: 0.6268 (ttpp) cc_final: 0.5988 (pttp) REVERT: M 20 SER cc_start: 0.9129 (p) cc_final: 0.8928 (p) REVERT: M 68 ARG cc_start: 0.9160 (mtp85) cc_final: 0.8739 (mtp85) REVERT: M 76 ILE cc_start: 0.8771 (mm) cc_final: 0.8519 (mm) REVERT: N 32 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8423 (tm-30) REVERT: N 47 GLU cc_start: 0.8094 (pm20) cc_final: 0.7825 (pm20) outliers start: 41 outliers final: 20 residues processed: 242 average time/residue: 0.5841 time to fit residues: 158.0519 Evaluate side-chains 228 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain U residue 39 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 56 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 131 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 97 GLN J 86 HIS N 59 HIS ** U 23 ASN ** 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 = 0.3524 r_free = 0.3524 target = 0.100648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.074962 restraints weight = 39532.057| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.63 r_work: 0.2936 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18727 Z= 0.196 Angle : 1.084 13.912 27602 Z= 0.438 Chirality : 0.088 0.752 3454 Planarity : 0.005 0.043 1764 Dihedral : 18.231 176.889 6746 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.79 % Favored : 93.88 % Rotamer: Outliers : 5.35 % Allowed : 24.87 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.29), residues: 915 helix: 1.30 (0.28), residues: 374 sheet: 0.13 (0.39), residues: 180 loop : -0.67 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 48 TYR 0.020 0.002 TYR J 170 PHE 0.012 0.001 PHE G 129 TRP 0.010 0.001 TRP J 70 HIS 0.007 0.001 HIS N 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 (18723) covalent geometry : angle 1.08184 / 0.44 (27596) hydrogen bonds : bond 0.06144 / 3.20 ( 718) hydrogen bonds : angle 3.62911 / 1.46 ( 1586) metal coordination : bond 0.00644 / 0.32 ( 4) metal coordination : angle 4.31465 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7638 (m-80) cc_final: 0.7218 (m-80) REVERT: E 85 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8039 (ttpp) REVERT: E 92 LYS cc_start: 0.9013 (ptpp) cc_final: 0.8449 (pmmt) REVERT: G 17 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8321 (m-30) REVERT: G 91 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: G 138 GLN cc_start: 0.8710 (tp-100) cc_final: 0.8314 (tp-100) REVERT: G 142 ASN cc_start: 0.8846 (m-40) cc_final: 0.8101 (m-40) REVERT: I 74 GLU cc_start: 0.8383 (pp20) cc_final: 0.8073 (pp20) REVERT: I 123 GLU cc_start: 0.9247 (tp30) cc_final: 0.8950 (mm-30) REVERT: I 149 ARG cc_start: 0.7595 (tmm-80) cc_final: 0.7389 (tmm-80) REVERT: J 79 ASP cc_start: 0.9309 (t0) cc_final: 0.8758 (t0) REVERT: M 5 LYS cc_start: 0.6146 (ttpp) cc_final: 0.5879 (ptmm) REVERT: M 20 SER cc_start: 0.9153 (p) cc_final: 0.8949 (p) REVERT: M 53 ARG cc_start: 0.8899 (mtm-85) cc_final: 0.8438 (mtt-85) REVERT: M 68 ARG cc_start: 0.9157 (mtp85) cc_final: 0.8693 (mtp85) REVERT: M 76 ILE cc_start: 0.8735 (mm) cc_final: 0.8466 (mm) REVERT: M 100 ILE cc_start: 0.8755 (mm) cc_final: 0.8512 (mt) REVERT: N 16 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: N 32 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8392 (tm-30) REVERT: N 115 LYS cc_start: 0.8071 (ptpp) cc_final: 0.7831 (ptmt) outliers start: 40 outliers final: 23 residues processed: 237 average time/residue: 0.5584 time to fit residues: 148.9282 Evaluate side-chains 236 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 16 GLU Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain U residue 79 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 97 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 27 GLN J 86 HIS ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 HIS U 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.096917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.070694 restraints weight = 39457.053| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.61 r_work: 0.2839 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 18727 Z= 0.312 Angle : 1.161 18.862 27602 Z= 0.471 Chirality : 0.095 0.922 3454 Planarity : 0.005 0.059 1764 Dihedral : 18.312 179.815 6746 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.23 % Favored : 93.44 % Rotamer: Outliers : 5.88 % Allowed : 26.87 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.29), residues: 915 helix: 1.24 (0.28), residues: 374 sheet: 0.05 (0.39), residues: 185 loop : -0.67 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 3 TYR 0.023 0.002 TYR J 170 PHE 0.013 0.002 PHE I 107 TRP 0.009 0.001 TRP J 70 HIS 0.006 0.001 HIS N 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.31 (18723) covalent geometry : angle 1.15914 / 0.47 (27596) hydrogen bonds : bond 0.06175 / 3.20 ( 718) hydrogen bonds : angle 3.67092 / 1.48 ( 1586) metal coordination : bond 0.00638 / 0.32 ( 4) metal coordination : angle 4.57937 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7774 (m-80) cc_final: 0.7318 (m-80) REVERT: E 85 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8136 (ttpp) REVERT: G 48 ARG cc_start: 0.8723 (mtp85) cc_final: 0.8483 (mtp85) REVERT: G 138 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8495 (tp40) REVERT: G 141 MET cc_start: 0.9158 (mmt) cc_final: 0.8747 (mmt) REVERT: G 142 ASN cc_start: 0.8841 (m-40) cc_final: 0.8316 (m-40) REVERT: G 169 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8082 (pp20) REVERT: I 74 GLU cc_start: 0.8465 (pp20) cc_final: 0.8075 (pp20) REVERT: I 123 GLU cc_start: 0.9270 (tp30) cc_final: 0.9028 (mm-30) REVERT: I 134 SER cc_start: 0.9282 (m) cc_final: 0.9081 (p) REVERT: I 149 ARG cc_start: 0.7731 (tmm-80) cc_final: 0.7434 (tmm-80) REVERT: J 44 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7926 (pmt) REVERT: J 79 ASP cc_start: 0.9315 (t0) cc_final: 0.8807 (t0) REVERT: J 108 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8115 (tmt-80) REVERT: M 5 LYS cc_start: 0.6175 (ttpp) cc_final: 0.5800 (pttp) REVERT: M 20 SER cc_start: 0.9180 (p) cc_final: 0.8966 (p) REVERT: M 68 ARG cc_start: 0.9178 (mtp85) cc_final: 0.8722 (mtp85) REVERT: M 76 ILE cc_start: 0.8814 (mm) cc_final: 0.8605 (mm) REVERT: M 100 ILE cc_start: 0.8698 (mm) cc_final: 0.8488 (mt) REVERT: N 16 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: N 32 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8436 (tm-30) REVERT: N 33 THR cc_start: 0.9376 (m) cc_final: 0.9035 (m) REVERT: N 47 GLU cc_start: 0.7991 (pm20) cc_final: 0.7654 (pm20) REVERT: N 115 LYS cc_start: 0.8176 (ptpp) cc_final: 0.7921 (ptmt) REVERT: S 37 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8413 (p90) outliers start: 44 outliers final: 25 residues processed: 233 average time/residue: 0.6145 time to fit residues: 160.2916 Evaluate side-chains 235 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 16 GLU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain S residue 37 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 27 GLN G 97 GLN J 86 HIS ** J 88 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 = 0.3489 r_free = 0.3489 target = 0.098561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.072870 restraints weight = 39449.966| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.60 r_work: 0.2876 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18727 Z= 0.245 Angle : 1.102 17.718 27602 Z= 0.447 Chirality : 0.090 0.846 3454 Planarity : 0.005 0.057 1764 Dihedral : 18.370 179.474 6746 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.57 % Favored : 94.10 % Rotamer: Outliers : 5.08 % Allowed : 28.74 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.29), residues: 915 helix: 1.28 (0.28), residues: 375 sheet: 0.02 (0.39), residues: 184 loop : -0.67 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 48 TYR 0.024 0.002 TYR J 170 PHE 0.010 0.001 PHE G 129 TRP 0.010 0.001 TRP J 70 HIS 0.007 0.001 HIS N 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.25 (18723) covalent geometry : angle 1.10061 / 0.45 (27596) hydrogen bonds : bond 0.06058 / 3.15 ( 718) hydrogen bonds : angle 3.62518 / 1.46 ( 1586) metal coordination : bond 0.00507 / 0.25 ( 4) metal coordination : angle 4.04734 / 1.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7649 (m-80) cc_final: 0.7071 (m-80) REVERT: E 85 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8042 (ttpp) REVERT: G 138 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8463 (tp40) REVERT: G 141 MET cc_start: 0.9160 (mmt) cc_final: 0.8705 (mmt) REVERT: G 142 ASN cc_start: 0.8886 (m-40) cc_final: 0.8337 (m-40) REVERT: G 169 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8069 (pp20) REVERT: I 74 GLU cc_start: 0.8483 (pp20) cc_final: 0.8069 (pp20) REVERT: I 123 GLU cc_start: 0.9271 (tp30) cc_final: 0.8925 (mm-30) REVERT: J 44 MET cc_start: 0.8136 (pmt) cc_final: 0.7900 (pmt) REVERT: J 79 ASP cc_start: 0.9322 (t0) cc_final: 0.8805 (t0) REVERT: M 5 LYS cc_start: 0.6140 (ttpp) cc_final: 0.5777 (pttp) REVERT: M 20 SER cc_start: 0.9133 (p) cc_final: 0.8913 (p) REVERT: M 53 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8608 (mtt-85) REVERT: M 68 ARG cc_start: 0.9157 (mtp85) cc_final: 0.8678 (mtp85) REVERT: M 76 ILE cc_start: 0.8806 (mm) cc_final: 0.8526 (mm) REVERT: N 16 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: N 32 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8419 (tm-30) REVERT: N 33 THR cc_start: 0.9364 (m) cc_final: 0.9006 (m) REVERT: N 115 LYS cc_start: 0.8071 (ptpp) cc_final: 0.7853 (ptmt) REVERT: S 35 ARG cc_start: 0.8975 (mtt180) cc_final: 0.8640 (mtt180) REVERT: U 39 MET cc_start: 0.9023 (ttm) cc_final: 0.8601 (ttm) outliers start: 38 outliers final: 25 residues processed: 227 average time/residue: 0.6027 time to fit residues: 152.3559 Evaluate side-chains 233 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 53 ARG Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 16 GLU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain N residue 103 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 88 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 8 HIS G 27 GLN J 86 HIS ** J 88 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 = 0.3497 r_free = 0.3497 target = 0.099070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.073148 restraints weight = 39273.354| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.59 r_work: 0.2891 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18727 Z= 0.231 Angle : 1.085 16.512 27602 Z= 0.441 Chirality : 0.088 0.809 3454 Planarity : 0.005 0.055 1764 Dihedral : 18.376 179.361 6744 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.79 % Favored : 93.88 % Rotamer: Outliers : 6.15 % Allowed : 28.61 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.29), residues: 915 helix: 1.33 (0.28), residues: 377 sheet: -0.01 (0.39), residues: 184 loop : -0.63 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 48 TYR 0.022 0.002 TYR J 170 PHE 0.009 0.001 PHE G 129 TRP 0.012 0.001 TRP J 70 HIS 0.007 0.001 HIS N 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.23 (18723) covalent geometry : angle 1.08328 / 0.44 (27596) hydrogen bonds : bond 0.06002 / 3.12 ( 718) hydrogen bonds : angle 3.60759 / 1.46 ( 1586) metal coordination : bond 0.00533 / 0.27 ( 4) metal coordination : angle 3.75926 / 1.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7675 (m-80) cc_final: 0.7037 (m-80) REVERT: E 85 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8016 (ttpp) REVERT: G 48 ARG cc_start: 0.8667 (mtp85) cc_final: 0.8443 (mtp85) REVERT: G 117 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: G 138 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8443 (tp40) REVERT: G 142 ASN cc_start: 0.8872 (m-40) cc_final: 0.8343 (m-40) REVERT: I 74 GLU cc_start: 0.8499 (pp20) cc_final: 0.8053 (pp20) REVERT: I 123 GLU cc_start: 0.9245 (tp30) cc_final: 0.8917 (mm-30) REVERT: J 44 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7952 (pmt) REVERT: J 79 ASP cc_start: 0.9311 (t0) cc_final: 0.8798 (t0) REVERT: J 108 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8148 (tmt-80) REVERT: J 130 ASN cc_start: 0.9048 (OUTLIER) cc_final: 0.8829 (t0) REVERT: M 5 LYS cc_start: 0.6214 (ttpp) cc_final: 0.5875 (pttt) REVERT: M 20 SER cc_start: 0.9113 (p) cc_final: 0.8880 (p) REVERT: M 53 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8652 (mtt-85) REVERT: M 68 ARG cc_start: 0.9157 (mtp85) cc_final: 0.8769 (mtp85) REVERT: M 100 ILE cc_start: 0.8728 (mm) cc_final: 0.8503 (mt) REVERT: N 16 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: N 32 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8438 (tm-30) REVERT: N 33 THR cc_start: 0.9366 (m) cc_final: 0.9005 (m) REVERT: N 47 GLU cc_start: 0.7951 (pm20) cc_final: 0.7664 (pm20) REVERT: S 35 ARG cc_start: 0.8920 (mtt180) cc_final: 0.8585 (mtt180) REVERT: U 39 MET cc_start: 0.8966 (ttm) cc_final: 0.8574 (ttm) outliers start: 46 outliers final: 27 residues processed: 232 average time/residue: 0.6089 time to fit residues: 157.8442 Evaluate side-chains 234 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 130 ASN Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 53 ARG Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 16 GLU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain U residue 28 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 53 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 27 GLN G 97 GLN J 86 HIS ** J 88 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 = 0.3550 r_free = 0.3550 target = 0.102010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.076334 restraints weight = 39588.803| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.59 r_work: 0.2966 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18727 Z= 0.174 Angle : 1.038 13.242 27602 Z= 0.423 Chirality : 0.083 0.694 3454 Planarity : 0.005 0.046 1764 Dihedral : 18.343 178.909 6744 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.57 % Favored : 94.10 % Rotamer: Outliers : 4.95 % Allowed : 30.48 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.29), residues: 915 helix: 1.41 (0.28), residues: 377 sheet: 0.15 (0.40), residues: 176 loop : -0.58 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 48 TYR 0.021 0.002 TYR J 170 PHE 0.010 0.001 PHE G 129 TRP 0.014 0.001 TRP J 70 HIS 0.008 0.001 HIS N 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (18723) covalent geometry : angle 1.03633 / 0.42 (27596) hydrogen bonds : bond 0.06045 / 3.14 ( 718) hydrogen bonds : angle 3.56786 / 1.45 ( 1586) metal coordination : bond 0.00461 / 0.23 ( 4) metal coordination : angle 3.61391 / 1.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 85 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8236 (ttpp) REVERT: E 92 LYS cc_start: 0.8951 (ptpp) cc_final: 0.8726 (pmmt) REVERT: G 99 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7645 (tm-30) REVERT: G 117 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: G 138 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8405 (tp40) REVERT: I 74 GLU cc_start: 0.8445 (pp20) cc_final: 0.7992 (pp20) REVERT: I 123 GLU cc_start: 0.9259 (tp30) cc_final: 0.8916 (mm-30) REVERT: J 44 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7884 (pmt) REVERT: J 79 ASP cc_start: 0.9313 (t0) cc_final: 0.8782 (t0) REVERT: J 108 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8124 (tmt-80) REVERT: M 5 LYS cc_start: 0.6038 (ttpp) cc_final: 0.5694 (ptmm) REVERT: M 20 SER cc_start: 0.9069 (p) cc_final: 0.8824 (p) REVERT: M 53 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8342 (mtt-85) REVERT: M 68 ARG cc_start: 0.9141 (mtp85) cc_final: 0.8760 (mtp85) REVERT: M 100 ILE cc_start: 0.8743 (mm) cc_final: 0.8515 (mt) REVERT: N 17 VAL cc_start: 0.9508 (m) cc_final: 0.9162 (p) REVERT: N 32 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8561 (tm-30) REVERT: N 47 GLU cc_start: 0.7986 (pm20) cc_final: 0.7672 (pm20) REVERT: U 39 MET cc_start: 0.8918 (ttm) cc_final: 0.8556 (ttm) outliers start: 37 outliers final: 21 residues processed: 238 average time/residue: 0.5720 time to fit residues: 152.4590 Evaluate side-chains 229 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 53 ARG Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain U residue 62 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 27 GLN J 86 HIS ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.075265 restraints weight = 39492.956| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.61 r_work: 0.2935 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18727 Z= 0.205 Angle : 1.054 14.841 27602 Z= 0.431 Chirality : 0.084 0.740 3454 Planarity : 0.005 0.044 1764 Dihedral : 18.313 179.480 6744 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.46 % Favored : 94.21 % Rotamer: Outliers : 4.55 % Allowed : 31.68 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.29), residues: 915 helix: 1.34 (0.27), residues: 377 sheet: 0.14 (0.40), residues: 176 loop : -0.56 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 48 TYR 0.026 0.002 TYR J 170 PHE 0.012 0.001 PHE G 10 TRP 0.018 0.001 TRP J 70 HIS 0.007 0.001 HIS N 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (18723) covalent geometry : angle 1.05315 / 0.43 (27596) hydrogen bonds : bond 0.05950 / 3.10 ( 718) hydrogen bonds : angle 3.56174 / 1.44 ( 1586) metal coordination : bond 0.00411 / 0.21 ( 4) metal coordination : angle 3.05022 / 1.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 85 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8047 (ttpp) REVERT: E 92 LYS cc_start: 0.8931 (ptpp) cc_final: 0.8727 (pmmt) REVERT: G 99 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7641 (tm-30) REVERT: G 117 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: G 138 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8473 (tp40) REVERT: I 74 GLU cc_start: 0.8482 (pp20) cc_final: 0.8029 (pp20) REVERT: I 90 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8443 (tp30) REVERT: I 123 GLU cc_start: 0.9237 (tp30) cc_final: 0.8918 (mm-30) REVERT: J 44 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7864 (pmt) REVERT: J 51 THR cc_start: 0.9258 (t) cc_final: 0.9034 (t) REVERT: J 79 ASP cc_start: 0.9315 (t0) cc_final: 0.8823 (t0) REVERT: J 108 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8129 (tmt-80) REVERT: M 5 LYS cc_start: 0.5622 (ttpp) cc_final: 0.5394 (ptmt) REVERT: M 20 SER cc_start: 0.9080 (p) cc_final: 0.8833 (p) REVERT: M 53 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8414 (mtt-85) REVERT: M 68 ARG cc_start: 0.9154 (mtp85) cc_final: 0.8777 (mtp85) REVERT: N 32 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8602 (tm-30) REVERT: N 47 GLU cc_start: 0.7939 (pm20) cc_final: 0.7635 (pm20) REVERT: S 46 GLU cc_start: 0.8878 (pt0) cc_final: 0.8546 (pt0) REVERT: U 39 MET cc_start: 0.8897 (ttm) cc_final: 0.8521 (ttm) outliers start: 34 outliers final: 21 residues processed: 218 average time/residue: 0.6370 time to fit residues: 154.6611 Evaluate side-chains 228 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 53 ARG Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain S residue 26 ARG Chi-restraints excluded: chain U residue 79 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 82 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN U 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.071641 restraints weight = 38884.680| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.50 r_work: 0.2864 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 18727 Z= 0.387 Angle : 1.229 20.687 27602 Z= 0.504 Chirality : 0.100 1.006 3454 Planarity : 0.006 0.055 1764 Dihedral : 18.482 179.831 6744 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.01 % Favored : 93.66 % Rotamer: Outliers : 4.68 % Allowed : 32.09 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.29), residues: 915 helix: 1.18 (0.27), residues: 371 sheet: -0.20 (0.39), residues: 184 loop : -0.55 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 11 TYR 0.029 0.003 TYR J 170 PHE 0.014 0.002 PHE G 192 TRP 0.015 0.002 TRP J 70 HIS 0.006 0.001 HIS M 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00812 / 0.39 (18723) covalent geometry : angle 1.22833 / 0.50 (27596) hydrogen bonds : bond 0.06369 / 3.30 ( 718) hydrogen bonds : angle 3.75247 / 1.52 ( 1586) metal coordination : bond 0.00405 / 0.20 ( 4) metal coordination : angle 3.30583 / 1.10 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 85 LYS cc_start: 0.8763 (ttmt) cc_final: 0.8219 (ttpp) REVERT: G 117 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: G 142 ASN cc_start: 0.8918 (m-40) cc_final: 0.8479 (m-40) REVERT: I 74 GLU cc_start: 0.8511 (pp20) cc_final: 0.8045 (pp20) REVERT: I 90 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8355 (tp30) REVERT: J 44 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7999 (pmt) REVERT: J 79 ASP cc_start: 0.9283 (t0) cc_final: 0.8911 (OUTLIER) REVERT: J 108 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8149 (tmt-80) REVERT: M 5 LYS cc_start: 0.5823 (ttpp) cc_final: 0.5512 (ptmm) REVERT: M 20 SER cc_start: 0.9202 (p) cc_final: 0.8941 (p) REVERT: M 53 ARG cc_start: 0.8927 (mtm-85) cc_final: 0.8653 (mtt-85) REVERT: M 68 ARG cc_start: 0.9123 (mtp85) cc_final: 0.8744 (mtp85) REVERT: N 32 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8523 (tm-30) REVERT: N 47 GLU cc_start: 0.7962 (pm20) cc_final: 0.7650 (pm20) REVERT: S 46 GLU cc_start: 0.8846 (pt0) cc_final: 0.8579 (pt0) REVERT: U 29 ASN cc_start: 0.8483 (t0) cc_final: 0.8168 (t0) REVERT: U 39 MET cc_start: 0.9084 (ttm) cc_final: 0.8766 (ttm) outliers start: 35 outliers final: 21 residues processed: 221 average time/residue: 0.5802 time to fit residues: 142.7338 Evaluate side-chains 221 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 117 GLN Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 86 HIS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain S residue 26 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 130 optimal weight: 0.1980 chunk 114 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 27 GLN J 86 HIS M 64 HIS U 69 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.078402 restraints weight = 39151.458| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.58 r_work: 0.3042 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18727 Z= 0.170 Angle : 1.053 12.059 27602 Z= 0.433 Chirality : 0.084 0.644 3454 Planarity : 0.005 0.046 1764 Dihedral : 18.417 179.501 6744 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.25 % Favored : 94.43 % Rotamer: Outliers : 3.34 % Allowed : 33.96 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.29), residues: 915 helix: 1.20 (0.27), residues: 377 sheet: 0.00 (0.39), residues: 180 loop : -0.63 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 41 TYR 0.024 0.002 TYR J 170 PHE 0.013 0.001 PHE U 74 TRP 0.019 0.001 TRP J 70 HIS 0.008 0.001 HIS N 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (18723) covalent geometry : angle 1.05224 / 0.43 (27596) hydrogen bonds : bond 0.06281 / 3.25 ( 718) hydrogen bonds : angle 3.64028 / 1.48 ( 1586) metal coordination : bond 0.00408 / 0.20 ( 4) metal coordination : angle 2.61834 / 0.87 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5864.50 seconds wall clock time: 100 minutes 48.03 seconds (6048.03 seconds total)