Starting phenix.real_space_refine on Thu Mar 5 00:07:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cvo_27011/03_2026/8cvo_27011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cvo_27011/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8cvo_27011/03_2026/8cvo_27011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cvo_27011/03_2026/8cvo_27011.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cvo_27011/03_2026/8cvo_27011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cvo_27011/03_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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': 471} 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 Unresolved non-hydrogen dihedrals: 2 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: 3.98, per 1000 atoms: 0.23 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: 1.34 Conformation dependent library (CDL) restraints added in 406.8 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: 2.70 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: 3.99 Time building geometry restraints manager: 1.56 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 - 2.75: 27289 2.75 - 5.50: 272 5.50 - 8.25: 28 8.25 - 11.00: 10 11.00 - 13.75: 3 Bond angle restraints: 27602 Sorted by residual: angle pdb=" C3' G A1184 " pdb=" O3' G A1184 " pdb=" P U A1185 " ideal model delta sigma weight residual 120.20 106.45 13.75 1.50e+00 4.44e-01 8.40e+01 angle pdb=" C3' U A1153 " pdb=" O3' U A1153 " pdb=" P C A1154 " ideal model delta sigma weight residual 120.20 108.99 11.21 1.50e+00 4.44e-01 5.58e+01 angle pdb=" C3' U A 958 " pdb=" O3' U A 958 " pdb=" P A A 959 " ideal model delta sigma weight residual 120.20 109.13 11.07 1.50e+00 4.44e-01 5.44e+01 angle pdb=" C3' A A1343 " pdb=" O3' A A1343 " pdb=" P U A1344 " ideal model delta sigma weight residual 120.20 109.89 10.31 1.50e+00 4.44e-01 4.72e+01 angle pdb=" C3' A A 959 " pdb=" O3' A A 959 " pdb=" P G A 960 " ideal model delta sigma weight residual 120.20 110.11 10.09 1.50e+00 4.44e-01 4.52e+01 ... (remaining 27597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 10803 35.87 - 71.75: 1182 71.75 - 107.62: 137 107.62 - 143.49: 3 143.49 - 179.36: 8 Dihedral angle restraints: 12133 sinusoidal: 9489 harmonic: 2644 Sorted by residual: dihedral pdb=" O4' C A1013 " pdb=" C1' C A1013 " pdb=" N1 C A1013 " pdb=" C2 C A1013 " ideal model delta sinusoidal sigma weight residual 200.00 48.36 151.64 1 1.50e+01 4.44e-03 8.02e+01 dihedral pdb=" O4' C A1144 " pdb=" C1' C A1144 " pdb=" N1 C A1144 " pdb=" C2 C A1144 " ideal model delta sinusoidal sigma weight residual 200.00 69.94 130.06 1 1.50e+01 4.44e-03 7.01e+01 dihedral pdb=" O4' U A1121 " pdb=" C1' U A1121 " pdb=" N1 U A1121 " pdb=" C2 U A1121 " ideal model delta sinusoidal sigma weight residual 232.00 52.64 179.36 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3266 0.085 - 0.170: 149 0.170 - 0.255: 19 0.255 - 0.340: 5 0.340 - 0.425: 15 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 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.51e+00 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 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.41e+00 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 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.25e+00 ... (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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 20.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:8.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 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= 0.244 Angle : 0.696 21.698 27608 Z= 0.381 Chirality : 0.047 0.425 3454 Planarity : 0.008 0.247 1764 Dihedral : 22.824 179.364 10435 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 covalent geometry : bond 0.00452 (18723) covalent geometry : angle 0.67373 (27602) hydrogen bonds : bond 0.18280 ( 718) hydrogen bonds : angle 6.51194 ( 1586) metal coordination : bond 0.05865 ( 4) metal coordination : angle 11.91809 ( 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 : 0.375 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: 0.6618 time to fit residues: 211.0537 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 : 0.391 ------------------------------------------------------------------------------- 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: 20.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3441 r_free = 0.3441 target = 0.096048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.070105 restraints weight = 39348.010| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.62 r_work: 0.2824 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18727 Z= 0.151 Angle : 0.621 9.835 27608 Z= 0.321 Chirality : 0.037 0.252 3454 Planarity : 0.005 0.041 1764 Dihedral : 23.484 178.520 8627 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.03 % Favored : 94.32 % Rotamer: Outliers : 3.61 % Allowed : 17.65 % Favored : 78.74 % 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: 0.32 (0.29), residues: 915 helix: 1.26 (0.28), residues: 373 sheet: -0.02 (0.40), residues: 178 loop : -0.69 (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 covalent geometry : bond 0.00301 (18723) covalent geometry : angle 0.61538 (27602) hydrogen bonds : bond 0.06060 ( 718) hydrogen bonds : angle 3.78536 ( 1586) metal coordination : bond 0.00779 ( 4) metal coordination : angle 5.46046 ( 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 265 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7187 (m-80) cc_final: 0.6683 (m-80) REVERT: E 85 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8431 (ttmt) REVERT: E 89 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8320 (tm-30) REVERT: G 17 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8290 (m-30) REVERT: G 138 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8258 (tp40) REVERT: G 142 ASN cc_start: 0.8839 (m-40) cc_final: 0.8455 (m110) REVERT: I 41 ASN cc_start: 0.9018 (t0) cc_final: 0.8808 (t0) REVERT: I 74 GLU cc_start: 0.8350 (pp20) cc_final: 0.8004 (pp20) REVERT: I 123 GLU cc_start: 0.9226 (tp30) cc_final: 0.8900 (mm-30) REVERT: J 79 ASP cc_start: 0.9270 (t0) cc_final: 0.8765 (t0) REVERT: J 80 TYR cc_start: 0.9165 (t80) cc_final: 0.8882 (t80) REVERT: J 92 GLU cc_start: 0.8453 (pp20) cc_final: 0.8191 (pp20) REVERT: J 169 GLN cc_start: 0.9454 (tt0) cc_final: 0.9201 (tt0) REVERT: M 20 SER cc_start: 0.9191 (p) cc_final: 0.8924 (p) REVERT: M 76 ILE cc_start: 0.8791 (mm) cc_final: 0.8581 (mm) REVERT: N 32 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8346 (tm-30) REVERT: N 50 ASP cc_start: 0.8837 (m-30) cc_final: 0.8630 (m-30) REVERT: N 58 ASP cc_start: 0.8460 (p0) cc_final: 0.8238 (p0) outliers start: 27 outliers final: 14 residues processed: 247 average time/residue: 0.5918 time to fit residues: 162.6730 Evaluate side-chains 230 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 125 ILE 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: 0.3980 chunk 97 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 47 optimal weight: 0.0020 chunk 74 optimal weight: 0.0770 chunk 93 optimal weight: 0.4980 chunk 59 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.1948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 148 ASN 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 = 0.3436 r_free = 0.3436 target = 0.095847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.069705 restraints weight = 39516.747| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.60 r_work: 0.2810 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18727 Z= 0.163 Angle : 0.588 9.435 27608 Z= 0.304 Chirality : 0.036 0.249 3454 Planarity : 0.004 0.043 1764 Dihedral : 23.333 178.171 8619 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.46 % Favored : 93.88 % Rotamer: Outliers : 4.81 % Allowed : 20.99 % Favored : 74.20 % 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: 1.33 (0.28), residues: 374 sheet: 0.00 (0.39), residues: 186 loop : -0.63 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 48 TYR 0.014 0.001 TYR G 167 PHE 0.011 0.001 PHE G 129 TRP 0.008 0.001 TRP G 22 HIS 0.006 0.001 HIS N 46 Details of bonding type rmsd covalent geometry : bond 0.00327 (18723) covalent geometry : angle 0.58285 (27602) hydrogen bonds : bond 0.05394 ( 718) hydrogen bonds : angle 3.63955 ( 1586) metal coordination : bond 0.00749 ( 4) metal coordination : angle 5.11816 ( 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 260 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7453 (m-80) cc_final: 0.6903 (m-80) REVERT: E 85 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8396 (ttmt) REVERT: G 17 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8337 (m-30) REVERT: G 48 ARG cc_start: 0.8766 (mtp85) cc_final: 0.8546 (mtp85) REVERT: G 138 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8379 (tp-100) REVERT: G 141 MET cc_start: 0.9237 (mmt) cc_final: 0.8932 (mmt) REVERT: I 74 GLU cc_start: 0.8413 (pp20) cc_final: 0.8127 (pp20) REVERT: I 75 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8832 (m) REVERT: I 123 GLU cc_start: 0.9227 (tp30) cc_final: 0.8927 (mm-30) REVERT: I 149 ARG cc_start: 0.7539 (tmm-80) cc_final: 0.7332 (tmm-80) REVERT: J 79 ASP cc_start: 0.9296 (t0) cc_final: 0.8804 (t0) REVERT: J 92 GLU cc_start: 0.8492 (pp20) cc_final: 0.8279 (pp20) REVERT: J 169 GLN cc_start: 0.9525 (tt0) cc_final: 0.9248 (tt0) REVERT: M 5 LYS cc_start: 0.6196 (ttpp) cc_final: 0.5939 (pttp) REVERT: M 20 SER cc_start: 0.9144 (p) cc_final: 0.8911 (p) REVERT: M 68 ARG cc_start: 0.9142 (mtp85) cc_final: 0.8937 (mtp85) REVERT: M 76 ILE cc_start: 0.8755 (mm) cc_final: 0.8484 (mm) REVERT: N 32 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8340 (tm-30) REVERT: N 47 GLU cc_start: 0.8122 (pm20) cc_final: 0.7837 (pm20) REVERT: N 50 ASP cc_start: 0.8830 (m-30) cc_final: 0.8628 (m-30) outliers start: 36 outliers final: 16 residues processed: 239 average time/residue: 0.5800 time to fit residues: 154.2878 Evaluate side-chains 226 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 ASP 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 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 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 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: 0.8980 chunk 98 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 97 GLN J 86 HIS ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.095986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.070041 restraints weight = 39461.887| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.62 r_work: 0.2813 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18727 Z= 0.173 Angle : 0.590 9.099 27608 Z= 0.306 Chirality : 0.037 0.251 3454 Planarity : 0.004 0.049 1764 Dihedral : 23.291 177.790 8619 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.68 % Favored : 93.99 % Rotamer: Outliers : 5.61 % Allowed : 23.66 % Favored : 70.72 % 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: 1.40 (0.28), residues: 374 sheet: 0.19 (0.39), residues: 180 loop : -0.58 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 48 TYR 0.013 0.001 TYR G 202 PHE 0.010 0.001 PHE U 74 TRP 0.009 0.001 TRP J 70 HIS 0.007 0.001 HIS N 46 Details of bonding type rmsd covalent geometry : bond 0.00349 (18723) covalent geometry : angle 0.58559 (27602) hydrogen bonds : bond 0.05215 ( 718) hydrogen bonds : angle 3.60655 ( 1586) metal coordination : bond 0.00624 ( 4) metal coordination : angle 4.70551 ( 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 255 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7540 (m-80) cc_final: 0.7119 (m-80) REVERT: E 85 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8154 (ttpt) REVERT: G 17 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8364 (m-30) REVERT: G 138 GLN cc_start: 0.8724 (tp-100) cc_final: 0.8339 (tp-100) REVERT: G 142 ASN cc_start: 0.8886 (m-40) cc_final: 0.8303 (m110) REVERT: I 74 GLU cc_start: 0.8415 (pp20) cc_final: 0.8091 (pp20) REVERT: I 75 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8802 (m) REVERT: I 123 GLU cc_start: 0.9266 (tp30) cc_final: 0.9026 (mm-30) REVERT: J 79 ASP cc_start: 0.9292 (t0) cc_final: 0.8758 (t0) REVERT: J 92 GLU cc_start: 0.8519 (pp20) cc_final: 0.8307 (pp20) REVERT: J 108 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8124 (tmt-80) REVERT: J 169 GLN cc_start: 0.9518 (tt0) cc_final: 0.9182 (tt0) REVERT: M 5 LYS cc_start: 0.6070 (ttpp) cc_final: 0.5750 (ptmm) REVERT: M 20 SER cc_start: 0.9133 (p) cc_final: 0.8925 (p) REVERT: M 68 ARG cc_start: 0.9101 (mtp85) cc_final: 0.8722 (mtp85) REVERT: M 76 ILE cc_start: 0.8730 (mm) cc_final: 0.8431 (mm) REVERT: N 16 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: N 32 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8447 (tm-30) REVERT: N 57 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8247 (tmm-80) outliers start: 42 outliers final: 16 residues processed: 230 average time/residue: 0.5793 time to fit residues: 148.4354 Evaluate side-chains 225 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 139 SER 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 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 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 57 ARG Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 97 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 GLN J 86 HIS ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.093053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.066698 restraints weight = 39372.567| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.67 r_work: 0.2739 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 18727 Z= 0.300 Angle : 0.655 8.451 27608 Z= 0.339 Chirality : 0.040 0.278 3454 Planarity : 0.005 0.063 1764 Dihedral : 23.312 175.682 8619 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.79 % Favored : 93.88 % Rotamer: Outliers : 5.88 % Allowed : 26.34 % Favored : 67.78 % 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: 0.47 (0.29), residues: 915 helix: 1.36 (0.28), residues: 374 sheet: 0.16 (0.39), residues: 180 loop : -0.66 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 3 TYR 0.020 0.002 TYR J 170 PHE 0.013 0.002 PHE U 74 TRP 0.009 0.001 TRP J 70 HIS 0.005 0.001 HIS S 31 Details of bonding type rmsd covalent geometry : bond 0.00598 (18723) covalent geometry : angle 0.65134 (27602) hydrogen bonds : bond 0.05608 ( 718) hydrogen bonds : angle 3.68385 ( 1586) metal coordination : bond 0.00457 ( 4) metal coordination : angle 4.58129 ( 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 253 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7751 (m-80) cc_final: 0.7282 (m-80) REVERT: E 85 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8086 (ttpp) REVERT: G 48 ARG cc_start: 0.8826 (mtp85) cc_final: 0.8555 (mtp85) REVERT: G 138 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8539 (tp40) REVERT: G 141 MET cc_start: 0.9176 (mmt) cc_final: 0.8734 (mmt) REVERT: G 169 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8044 (pp20) REVERT: I 74 GLU cc_start: 0.8426 (pp20) cc_final: 0.8057 (pp20) REVERT: J 79 ASP cc_start: 0.9316 (t0) cc_final: 0.8790 (t0) REVERT: J 106 ILE cc_start: 0.9416 (mt) cc_final: 0.9213 (mp) REVERT: J 108 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8115 (tmt-80) REVERT: J 150 ASP cc_start: 0.8689 (p0) cc_final: 0.7960 (p0) REVERT: J 169 GLN cc_start: 0.9549 (tt0) cc_final: 0.9228 (tt0) REVERT: M 5 LYS cc_start: 0.6193 (ttpp) cc_final: 0.5810 (pttp) REVERT: M 20 SER cc_start: 0.9130 (p) cc_final: 0.8846 (p) REVERT: M 68 ARG cc_start: 0.9157 (mtp85) cc_final: 0.8887 (mtp85) REVERT: N 16 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: N 32 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8407 (tm-30) REVERT: N 33 THR cc_start: 0.9351 (m) cc_final: 0.8978 (m) REVERT: N 47 GLU cc_start: 0.8094 (pm20) cc_final: 0.7791 (pm20) REVERT: N 57 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8255 (tmm-80) REVERT: S 37 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8349 (p90) outliers start: 44 outliers final: 25 residues processed: 234 average time/residue: 0.5880 time to fit residues: 153.1245 Evaluate side-chains 236 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 146 LEU 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 89 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 108 ARG 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 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 57 ARG Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain U residue 38 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 GLN G 97 GLN J 86 HIS ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.066982 restraints weight = 39432.538| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.66 r_work: 0.2751 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18727 Z= 0.262 Angle : 0.642 8.692 27608 Z= 0.333 Chirality : 0.040 0.271 3454 Planarity : 0.005 0.061 1764 Dihedral : 23.312 173.247 8619 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.90 % Favored : 93.77 % Rotamer: Outliers : 6.02 % Allowed : 26.74 % 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: 0.44 (0.29), residues: 915 helix: 1.36 (0.28), residues: 374 sheet: 0.08 (0.39), residues: 185 loop : -0.68 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 48 TYR 0.023 0.002 TYR J 170 PHE 0.012 0.002 PHE I 107 TRP 0.010 0.001 TRP J 70 HIS 0.006 0.001 HIS N 46 Details of bonding type rmsd covalent geometry : bond 0.00526 (18723) covalent geometry : angle 0.63890 (27602) hydrogen bonds : bond 0.05433 ( 718) hydrogen bonds : angle 3.67474 ( 1586) metal coordination : bond 0.00373 ( 4) metal coordination : angle 4.08163 ( 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 259 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7754 (m-80) cc_final: 0.7229 (m-80) REVERT: E 85 LYS cc_start: 0.8736 (ttmt) cc_final: 0.8092 (ttpp) REVERT: G 138 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8579 (tm-30) REVERT: G 141 MET cc_start: 0.9175 (mmt) cc_final: 0.8768 (mmt) REVERT: G 142 ASN cc_start: 0.8933 (m-40) cc_final: 0.8575 (m-40) REVERT: G 169 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8099 (pp20) REVERT: I 74 GLU cc_start: 0.8461 (pp20) cc_final: 0.8074 (pp20) REVERT: I 123 GLU cc_start: 0.9287 (tp30) cc_final: 0.9044 (mm-30) REVERT: I 134 SER cc_start: 0.9286 (m) cc_final: 0.9066 (p) REVERT: J 79 ASP cc_start: 0.9328 (t0) cc_final: 0.8800 (t0) REVERT: J 108 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7953 (tmt-80) REVERT: J 150 ASP cc_start: 0.8701 (p0) cc_final: 0.7993 (p0) REVERT: J 169 GLN cc_start: 0.9542 (tt0) cc_final: 0.9201 (tt0) REVERT: M 5 LYS cc_start: 0.6175 (ttpp) cc_final: 0.5843 (ptmm) REVERT: M 20 SER cc_start: 0.9115 (p) cc_final: 0.8879 (p) REVERT: M 53 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8630 (mtt-85) REVERT: M 68 ARG cc_start: 0.9145 (mtp85) cc_final: 0.8843 (mtp85) REVERT: M 76 ILE cc_start: 0.8521 (mm) cc_final: 0.8209 (mm) REVERT: N 16 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8308 (tt0) REVERT: N 32 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8429 (tm-30) REVERT: N 33 THR cc_start: 0.9360 (m) cc_final: 0.8985 (m) REVERT: N 57 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8242 (tmm-80) REVERT: U 39 MET cc_start: 0.9057 (ttm) cc_final: 0.8682 (ttm) outliers start: 45 outliers final: 26 residues processed: 235 average time/residue: 0.5969 time to fit residues: 155.9589 Evaluate side-chains 239 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 13 MET Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 89 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 108 ARG Chi-restraints excluded: chain J residue 125 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 16 GLU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain U residue 38 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 8 HIS G 27 GLN J 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.093559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.067284 restraints weight = 39252.377| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.64 r_work: 0.2748 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18727 Z= 0.264 Angle : 0.647 9.461 27608 Z= 0.336 Chirality : 0.040 0.271 3454 Planarity : 0.005 0.061 1764 Dihedral : 23.310 172.259 8617 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.34 % Favored : 93.33 % Rotamer: Outliers : 6.55 % Allowed : 27.67 % Favored : 65.78 % 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: 0.43 (0.29), residues: 915 helix: 1.35 (0.28), residues: 374 sheet: 0.06 (0.39), residues: 184 loop : -0.66 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 48 TYR 0.023 0.002 TYR J 170 PHE 0.011 0.002 PHE I 107 TRP 0.012 0.001 TRP J 70 HIS 0.006 0.001 HIS N 46 Details of bonding type rmsd covalent geometry : bond 0.00527 (18723) covalent geometry : angle 0.64551 (27602) hydrogen bonds : bond 0.05431 ( 718) hydrogen bonds : angle 3.68342 ( 1586) metal coordination : bond 0.00346 ( 4) metal coordination : angle 3.35754 ( 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 261 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 212 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7706 (m-80) cc_final: 0.7111 (m-80) REVERT: E 85 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8045 (ttpp) REVERT: G 48 ARG cc_start: 0.8799 (mtp85) cc_final: 0.8561 (mtp85) REVERT: G 117 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: G 138 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8536 (tp40) REVERT: G 141 MET cc_start: 0.9165 (mmt) cc_final: 0.8702 (mmt) REVERT: G 142 ASN cc_start: 0.8926 (m-40) cc_final: 0.8484 (m-40) REVERT: G 169 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8069 (pp20) REVERT: I 74 GLU cc_start: 0.8465 (pp20) cc_final: 0.8043 (pp20) REVERT: I 123 GLU cc_start: 0.9284 (tp30) cc_final: 0.8983 (mm-30) REVERT: J 79 ASP cc_start: 0.9320 (t0) cc_final: 0.8811 (t0) REVERT: J 108 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8157 (tmt-80) REVERT: J 150 ASP cc_start: 0.8691 (p0) cc_final: 0.7987 (p0) REVERT: M 5 LYS cc_start: 0.6236 (ttpp) cc_final: 0.5810 (ptmt) REVERT: M 20 SER cc_start: 0.9116 (p) cc_final: 0.8877 (p) REVERT: M 53 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8623 (mtt-85) REVERT: M 68 ARG cc_start: 0.9154 (mtp85) cc_final: 0.8837 (mtp85) REVERT: N 16 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: N 32 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: N 33 THR cc_start: 0.9382 (m) cc_final: 0.9021 (m) REVERT: N 47 GLU cc_start: 0.8021 (pm20) cc_final: 0.7737 (pm20) REVERT: N 57 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8232 (tmm-80) REVERT: U 39 MET cc_start: 0.9154 (ttm) cc_final: 0.8809 (ttm) outliers start: 49 outliers final: 29 residues processed: 237 average time/residue: 0.5575 time to fit residues: 147.5577 Evaluate side-chains 242 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 117 GLN 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 13 MET 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 89 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 108 ARG Chi-restraints excluded: chain J residue 125 ILE 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 16 GLU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain U residue 38 SER Chi-restraints excluded: chain U residue 60 VAL Chi-restraints excluded: chain U residue 79 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 53 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 GLN J 86 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.095746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.069389 restraints weight = 39320.048| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.63 r_work: 0.2812 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18727 Z= 0.161 Angle : 0.610 9.138 27608 Z= 0.316 Chirality : 0.037 0.249 3454 Planarity : 0.005 0.054 1764 Dihedral : 23.291 172.925 8617 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.25 % Favored : 94.43 % Rotamer: Outliers : 4.68 % Allowed : 30.61 % Favored : 64.71 % 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: 0.49 (0.29), residues: 915 helix: 1.37 (0.28), residues: 377 sheet: 0.01 (0.39), residues: 184 loop : -0.57 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 48 TYR 0.020 0.002 TYR J 170 PHE 0.010 0.001 PHE G 129 TRP 0.014 0.001 TRP J 70 HIS 0.007 0.001 HIS N 46 Details of bonding type rmsd covalent geometry : bond 0.00328 (18723) covalent geometry : angle 0.60885 (27602) hydrogen bonds : bond 0.05124 ( 718) hydrogen bonds : angle 3.63520 ( 1586) metal coordination : bond 0.00373 ( 4) metal coordination : angle 2.71249 ( 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 246 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 85 LYS cc_start: 0.8688 (ttmt) cc_final: 0.8267 (ttpp) REVERT: G 99 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7620 (tm-30) REVERT: G 117 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: G 138 GLN cc_start: 0.8770 (tp-100) cc_final: 0.8506 (tm-30) REVERT: G 142 ASN cc_start: 0.8900 (m-40) cc_final: 0.8493 (m-40) REVERT: I 74 GLU cc_start: 0.8452 (pp20) cc_final: 0.8049 (pp20) REVERT: I 123 GLU cc_start: 0.9263 (tp30) cc_final: 0.9005 (mm-30) REVERT: J 79 ASP cc_start: 0.9321 (t0) cc_final: 0.8793 (t0) REVERT: J 88 GLN cc_start: 0.7413 (pm20) cc_final: 0.7063 (pp30) REVERT: J 108 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8152 (tmt-80) REVERT: J 109 ILE cc_start: 0.9188 (mm) cc_final: 0.8921 (mp) REVERT: M 5 LYS cc_start: 0.6265 (ttpp) cc_final: 0.5844 (ptmm) REVERT: M 20 SER cc_start: 0.9126 (p) cc_final: 0.8884 (p) REVERT: M 53 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8607 (mtt-85) REVERT: M 68 ARG cc_start: 0.9132 (mtp85) cc_final: 0.8808 (mtp85) REVERT: M 100 ILE cc_start: 0.8736 (mm) cc_final: 0.8507 (mt) REVERT: N 16 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: N 32 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8432 (tm-30) REVERT: N 33 THR cc_start: 0.9365 (m) cc_final: 0.9006 (m) REVERT: N 47 GLU cc_start: 0.8027 (pm20) cc_final: 0.7682 (pm20) REVERT: N 57 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8212 (tmm-80) REVERT: U 39 MET cc_start: 0.9052 (ttm) cc_final: 0.8703 (ttm) outliers start: 35 outliers final: 22 residues processed: 228 average time/residue: 0.5633 time to fit residues: 143.1126 Evaluate side-chains 228 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 117 GLN 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 131 LEU 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 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 74 ILE 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 32 GLU Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 72 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 85 optimal weight: 0.0670 chunk 34 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 GLN G 97 GLN J 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.096028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.069882 restraints weight = 39264.688| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.60 r_work: 0.2818 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18727 Z= 0.162 Angle : 0.612 9.913 27608 Z= 0.316 Chirality : 0.036 0.249 3454 Planarity : 0.005 0.048 1764 Dihedral : 23.244 173.215 8617 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.79 % Favored : 93.88 % Rotamer: Outliers : 4.28 % Allowed : 31.55 % Favored : 64.17 % 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: 0.54 (0.29), residues: 915 helix: 1.41 (0.28), residues: 377 sheet: 0.07 (0.39), residues: 181 loop : -0.55 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 48 TYR 0.020 0.001 TYR G 202 PHE 0.010 0.001 PHE G 129 TRP 0.021 0.001 TRP J 70 HIS 0.008 0.001 HIS N 46 Details of bonding type rmsd covalent geometry : bond 0.00332 (18723) covalent geometry : angle 0.61009 (27602) hydrogen bonds : bond 0.05034 ( 718) hydrogen bonds : angle 3.60238 ( 1586) metal coordination : bond 0.00358 ( 4) metal coordination : angle 3.24102 ( 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 241 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 85 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8178 (ttpp) REVERT: E 89 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8998 (mm-30) REVERT: E 92 LYS cc_start: 0.8942 (ptpp) cc_final: 0.8673 (pmtt) REVERT: G 99 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7663 (tm-30) REVERT: G 117 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: G 138 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8440 (tp40) REVERT: I 74 GLU cc_start: 0.8508 (pp20) cc_final: 0.8063 (pp20) REVERT: I 123 GLU cc_start: 0.9242 (tp30) cc_final: 0.9021 (mm-30) REVERT: J 79 ASP cc_start: 0.9330 (t0) cc_final: 0.8845 (t0) REVERT: J 88 GLN cc_start: 0.7525 (pm20) cc_final: 0.7132 (pp30) REVERT: J 108 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8113 (tmt-80) REVERT: M 5 LYS cc_start: 0.6127 (ttpp) cc_final: 0.5878 (ptmm) REVERT: M 20 SER cc_start: 0.9135 (p) cc_final: 0.8892 (p) REVERT: M 53 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8380 (mtt-85) REVERT: M 68 ARG cc_start: 0.9134 (mtp85) cc_final: 0.8816 (mtp85) REVERT: M 100 ILE cc_start: 0.8816 (mm) cc_final: 0.8584 (mt) REVERT: N 16 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: N 32 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8529 (tm-30) REVERT: N 33 THR cc_start: 0.9340 (m) cc_final: 0.8976 (m) REVERT: N 47 GLU cc_start: 0.8032 (pm20) cc_final: 0.7806 (pm20) REVERT: N 57 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8153 (tmm-80) REVERT: S 46 GLU cc_start: 0.8852 (pt0) cc_final: 0.8565 (pt0) REVERT: U 39 MET cc_start: 0.8975 (ttm) cc_final: 0.8661 (ttm) outliers start: 32 outliers final: 19 residues processed: 224 average time/residue: 0.6056 time to fit residues: 150.6500 Evaluate side-chains 231 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 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 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 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 32 GLU Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain U residue 28 HIS 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: 2.9990 chunk 75 optimal weight: 0.0870 chunk 51 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 65 optimal weight: 0.0270 chunk 5 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 2.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 HIS S 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.095319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.068577 restraints weight = 38548.801| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.67 r_work: 0.2809 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 18727 Z= 0.289 Angle : 0.683 11.262 27608 Z= 0.352 Chirality : 0.040 0.273 3454 Planarity : 0.005 0.052 1764 Dihedral : 23.255 172.413 8617 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.01 % Favored : 93.66 % Rotamer: Outliers : 4.28 % Allowed : 32.89 % Favored : 62.83 % 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: 0.36 (0.29), residues: 915 helix: 1.35 (0.28), residues: 375 sheet: -0.17 (0.39), residues: 185 loop : -0.66 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 62 TYR 0.025 0.002 TYR J 170 PHE 0.011 0.002 PHE U 74 TRP 0.024 0.002 TRP J 70 HIS 0.005 0.001 HIS N 46 Details of bonding type rmsd covalent geometry : bond 0.00584 (18723) covalent geometry : angle 0.68174 (27602) hydrogen bonds : bond 0.05404 ( 718) hydrogen bonds : angle 3.70011 ( 1586) metal coordination : bond 0.00365 ( 4) metal coordination : angle 3.08110 ( 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 242 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 85 LYS cc_start: 0.8730 (ttmt) cc_final: 0.8034 (ttpp) REVERT: G 99 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7821 (tm-30) REVERT: G 117 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: I 74 GLU cc_start: 0.8499 (pp20) cc_final: 0.8063 (pp20) REVERT: I 123 GLU cc_start: 0.9170 (tp30) cc_final: 0.8904 (mm-30) REVERT: J 79 ASP cc_start: 0.9285 (t0) cc_final: 0.8928 (t0) REVERT: J 108 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8215 (tmt-80) REVERT: M 5 LYS cc_start: 0.6036 (ttpp) cc_final: 0.5641 (ptmt) REVERT: M 20 SER cc_start: 0.9199 (p) cc_final: 0.8968 (p) REVERT: M 53 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8647 (mtt-85) REVERT: M 68 ARG cc_start: 0.9200 (mtp85) cc_final: 0.8908 (mtp85) REVERT: M 100 ILE cc_start: 0.8815 (mm) cc_final: 0.8513 (mt) REVERT: N 16 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: N 32 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8483 (tm-30) REVERT: N 33 THR cc_start: 0.9365 (m) cc_final: 0.8995 (m) REVERT: N 47 GLU cc_start: 0.7957 (pm20) cc_final: 0.7754 (pm20) REVERT: N 57 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8262 (tmm-80) REVERT: S 46 GLU cc_start: 0.8852 (pt0) cc_final: 0.8586 (pt0) REVERT: U 29 ASN cc_start: 0.8411 (t0) cc_final: 0.8131 (t0) REVERT: U 39 MET cc_start: 0.8963 (ttm) cc_final: 0.8646 (ttm) outliers start: 32 outliers final: 19 residues processed: 226 average time/residue: 0.6242 time to fit residues: 156.7741 Evaluate side-chains 230 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 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 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 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 16 GLU Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain S residue 44 LEU 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 28 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 130 optimal weight: 0.0870 chunk 114 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 GLN J 86 HIS S 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.099500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.073177 restraints weight = 38839.154| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.62 r_work: 0.2924 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18727 Z= 0.134 Angle : 0.629 11.949 27608 Z= 0.324 Chirality : 0.036 0.242 3454 Planarity : 0.005 0.045 1764 Dihedral : 23.214 173.535 8617 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.03 % Favored : 94.64 % Rotamer: Outliers : 3.74 % Allowed : 34.22 % Favored : 62.03 % 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: 0.43 (0.29), residues: 915 helix: 1.28 (0.27), residues: 377 sheet: 0.07 (0.40), residues: 178 loop : -0.59 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 62 TYR 0.024 0.002 TYR J 170 PHE 0.012 0.001 PHE G 129 TRP 0.023 0.001 TRP J 70 HIS 0.008 0.001 HIS N 46 Details of bonding type rmsd covalent geometry : bond 0.00278 (18723) covalent geometry : angle 0.62717 (27602) hydrogen bonds : bond 0.05092 ( 718) hydrogen bonds : angle 3.62996 ( 1586) metal coordination : bond 0.00377 ( 4) metal coordination : angle 2.89885 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5955.67 seconds wall clock time: 102 minutes 6.31 seconds (6126.31 seconds total)