Starting phenix.real_space_refine on Fri Aug 22 23:37:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cnk_16759/08_2025/8cnk_16759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cnk_16759/08_2025/8cnk_16759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cnk_16759/08_2025/8cnk_16759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cnk_16759/08_2025/8cnk_16759.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cnk_16759/08_2025/8cnk_16759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cnk_16759/08_2025/8cnk_16759.map" } resolution = 2.97 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= 0.003 sd= 0.038 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5940 2.51 5 N 1325 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8850 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1758 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "B" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1758 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "C" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1758 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "D" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1758 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "E" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1758 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'DKA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.73, per 1000 atoms: 0.20 Number of scatterers: 8850 At special positions: 0 Unit cell: (102.208, 102.208, 67.4769, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1530 8.00 N 1325 7.00 C 5940 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: 0.45 Conformation dependent library (CDL) restraints added in 301.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 89.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 28 through 51 removed outlier: 3.558A pdb=" N VAL A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 59 through 87 removed outlier: 3.979A pdb=" N TYR A 79 " --> pdb=" O TRP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 118 Proline residue: A 104 - end of helix removed outlier: 3.914A pdb=" N PHE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 144 removed outlier: 4.224A pdb=" N LYS A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 169 removed outlier: 3.572A pdb=" N LEU A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 4.047A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 199 through 210 removed outlier: 3.560A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 232 Processing helix chain 'A' and resid 233 through 251 Processing helix chain 'B' and resid 28 through 51 removed outlier: 3.558A pdb=" N VAL B 32 " --> pdb=" O ASP B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 55 removed outlier: 3.620A pdb=" N VAL B 55 " --> pdb=" O ARG B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 52 through 55' Processing helix chain 'B' and resid 59 through 87 removed outlier: 3.979A pdb=" N TYR B 79 " --> pdb=" O TRP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 118 Proline residue: B 104 - end of helix removed outlier: 3.914A pdb=" N PHE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 144 removed outlier: 4.224A pdb=" N LYS B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 169 removed outlier: 3.572A pdb=" N LEU B 167 " --> pdb=" O MET B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 4.048A pdb=" N THR B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 199 through 210 removed outlier: 3.561A pdb=" N VAL B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 232 Processing helix chain 'B' and resid 233 through 251 Processing helix chain 'C' and resid 28 through 51 removed outlier: 3.542A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 59 through 87 removed outlier: 3.979A pdb=" N TYR C 79 " --> pdb=" O TRP C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 118 removed outlier: 3.511A pdb=" N ASP C 98 " --> pdb=" O PHE C 94 " (cutoff:3.500A) Proline residue: C 104 - end of helix removed outlier: 3.914A pdb=" N PHE C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 144 removed outlier: 4.224A pdb=" N LYS C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 169 removed outlier: 3.572A pdb=" N LEU C 167 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 4.048A pdb=" N THR C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 199 through 210 removed outlier: 3.560A pdb=" N VAL C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 232 Processing helix chain 'C' and resid 233 through 251 Processing helix chain 'D' and resid 28 through 51 removed outlier: 3.558A pdb=" N VAL D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 59 through 87 removed outlier: 3.979A pdb=" N TYR D 79 " --> pdb=" O TRP D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 118 Proline residue: D 104 - end of helix removed outlier: 3.915A pdb=" N PHE D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 144 removed outlier: 4.223A pdb=" N LYS D 126 " --> pdb=" O GLY D 122 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 169 removed outlier: 3.572A pdb=" N LEU D 167 " --> pdb=" O MET D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 4.047A pdb=" N THR D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 199 through 210 removed outlier: 3.560A pdb=" N VAL D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 232 Processing helix chain 'D' and resid 233 through 251 Processing helix chain 'E' and resid 28 through 51 removed outlier: 3.558A pdb=" N VAL E 32 " --> pdb=" O ASP E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 59 through 87 removed outlier: 3.979A pdb=" N TYR E 79 " --> pdb=" O TRP E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 118 Proline residue: E 104 - end of helix removed outlier: 3.915A pdb=" N PHE E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 144 removed outlier: 4.224A pdb=" N LYS E 126 " --> pdb=" O GLY E 122 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS E 127 " --> pdb=" O SER E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 169 removed outlier: 3.571A pdb=" N LEU E 167 " --> pdb=" O MET E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 178 removed outlier: 4.047A pdb=" N THR E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 196 Processing helix chain 'E' and resid 199 through 210 removed outlier: 3.560A pdb=" N VAL E 203 " --> pdb=" O ALA E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 232 Processing helix chain 'E' and resid 233 through 251 729 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1330 1.31 - 1.43: 2729 1.43 - 1.56: 4951 1.56 - 1.68: 0 1.68 - 1.81: 95 Bond restraints: 9105 Sorted by residual: bond pdb=" C PHE B 94 " pdb=" O PHE B 94 " ideal model delta sigma weight residual 1.236 1.182 0.055 1.26e-02 6.30e+03 1.88e+01 bond pdb=" C PHE D 94 " pdb=" O PHE D 94 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.26e-02 6.30e+03 1.84e+01 bond pdb=" C PHE E 94 " pdb=" O PHE E 94 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.26e-02 6.30e+03 1.83e+01 bond pdb=" C PHE A 94 " pdb=" O PHE A 94 " ideal model delta sigma weight residual 1.236 1.184 0.053 1.26e-02 6.30e+03 1.74e+01 bond pdb=" C PHE C 94 " pdb=" O PHE C 94 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.26e-02 6.30e+03 1.72e+01 ... (remaining 9100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12210 1.95 - 3.91: 124 3.91 - 5.86: 50 5.86 - 7.81: 26 7.81 - 9.76: 5 Bond angle restraints: 12415 Sorted by residual: angle pdb=" C ASP D 23 " pdb=" N LEU D 24 " pdb=" CA LEU D 24 " ideal model delta sigma weight residual 120.75 130.51 -9.76 1.51e+00 4.39e-01 4.18e+01 angle pdb=" C ASP E 23 " pdb=" N LEU E 24 " pdb=" CA LEU E 24 " ideal model delta sigma weight residual 120.75 130.50 -9.75 1.51e+00 4.39e-01 4.17e+01 angle pdb=" C ASP A 23 " pdb=" N LEU A 24 " pdb=" CA LEU A 24 " ideal model delta sigma weight residual 120.75 130.49 -9.74 1.51e+00 4.39e-01 4.16e+01 angle pdb=" C ASP B 23 " pdb=" N LEU B 24 " pdb=" CA LEU B 24 " ideal model delta sigma weight residual 120.75 130.48 -9.73 1.51e+00 4.39e-01 4.15e+01 angle pdb=" C ASP C 23 " pdb=" N LEU C 24 " pdb=" CA LEU C 24 " ideal model delta sigma weight residual 120.75 130.47 -9.72 1.51e+00 4.39e-01 4.15e+01 ... (remaining 12410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.00: 4575 12.00 - 23.99: 336 23.99 - 35.99: 117 35.99 - 47.99: 22 47.99 - 59.98: 20 Dihedral angle restraints: 5070 sinusoidal: 1830 harmonic: 3240 Sorted by residual: dihedral pdb=" C PHE D 94 " pdb=" N PHE D 94 " pdb=" CA PHE D 94 " pdb=" CB PHE D 94 " ideal model delta harmonic sigma weight residual -122.60 -114.46 -8.14 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" C PHE C 94 " pdb=" N PHE C 94 " pdb=" CA PHE C 94 " pdb=" CB PHE C 94 " ideal model delta harmonic sigma weight residual -122.60 -114.61 -7.99 0 2.50e+00 1.60e-01 1.02e+01 dihedral pdb=" C PHE B 94 " pdb=" N PHE B 94 " pdb=" CA PHE B 94 " pdb=" CB PHE B 94 " ideal model delta harmonic sigma weight residual -122.60 -114.73 -7.87 0 2.50e+00 1.60e-01 9.91e+00 ... (remaining 5067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1073 0.038 - 0.077: 275 0.077 - 0.115: 52 0.115 - 0.153: 0 0.153 - 0.192: 10 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CG LEU B 24 " pdb=" CB LEU B 24 " pdb=" CD1 LEU B 24 " pdb=" CD2 LEU B 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CA PHE C 94 " pdb=" N PHE C 94 " pdb=" C PHE C 94 " pdb=" CB PHE C 94 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CG LEU D 24 " pdb=" CB LEU D 24 " pdb=" CD1 LEU D 24 " pdb=" CD2 LEU D 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 1407 not shown) Planarity restraints: 1475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DKA A 301 " -0.084 2.00e-02 2.50e+03 4.85e-02 2.36e+01 pdb=" C2 DKA A 301 " 0.024 2.00e-02 2.50e+03 pdb=" O1 DKA A 301 " 0.030 2.00e-02 2.50e+03 pdb=" O2 DKA A 301 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 DKA C 301 " 0.084 2.00e-02 2.50e+03 4.85e-02 2.35e+01 pdb=" C2 DKA C 301 " -0.024 2.00e-02 2.50e+03 pdb=" O1 DKA C 301 " -0.030 2.00e-02 2.50e+03 pdb=" O2 DKA C 301 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 DKA D 301 " 0.084 2.00e-02 2.50e+03 4.85e-02 2.35e+01 pdb=" C2 DKA D 301 " -0.024 2.00e-02 2.50e+03 pdb=" O1 DKA D 301 " -0.030 2.00e-02 2.50e+03 pdb=" O2 DKA D 301 " -0.029 2.00e-02 2.50e+03 ... (remaining 1472 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2650 2.81 - 3.33: 9061 3.33 - 3.86: 14999 3.86 - 4.38: 18386 4.38 - 4.90: 30618 Nonbonded interactions: 75714 Sorted by model distance: nonbonded pdb=" O PHE B 34 " pdb=" OG1 THR B 38 " model vdw 2.290 3.040 nonbonded pdb=" O PHE A 34 " pdb=" OG1 THR A 38 " model vdw 2.291 3.040 nonbonded pdb=" O PHE D 34 " pdb=" OG1 THR D 38 " model vdw 2.291 3.040 nonbonded pdb=" O PHE C 34 " pdb=" OG1 THR C 38 " model vdw 2.291 3.040 nonbonded pdb=" O PHE E 34 " pdb=" OG1 THR E 38 " model vdw 2.291 3.040 ... (remaining 75709 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 6.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 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 0.070 9105 Z= 0.262 Angle : 0.664 9.764 12415 Z= 0.391 Chirality : 0.037 0.192 1410 Planarity : 0.005 0.049 1475 Dihedral : 10.654 59.981 3010 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % 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 aren not related in a simple way. whole: 1.09 (0.25), residues: 1100 helix: 0.87 (0.17), residues: 945 sheet: None (None), residues: 0 loop : 0.46 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 52 TYR 0.006 0.001 TYR E 192 PHE 0.037 0.002 PHE E 94 TRP 0.007 0.001 TRP B 75 HIS 0.000 0.000 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9105) covalent geometry : angle 0.66351 (12415) hydrogen bonds : bond 0.24353 ( 729) hydrogen bonds : angle 7.06538 ( 2187) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.209 Fit side-chains REVERT: A 147 MET cc_start: 0.6930 (ttt) cc_final: 0.6389 (ttt) REVERT: A 220 LEU cc_start: 0.8055 (tt) cc_final: 0.7812 (tp) REVERT: A 234 LEU cc_start: 0.8326 (tp) cc_final: 0.8118 (tt) REVERT: B 147 MET cc_start: 0.7153 (ttt) cc_final: 0.6635 (ttt) REVERT: B 220 LEU cc_start: 0.8092 (tt) cc_final: 0.7885 (tp) REVERT: C 147 MET cc_start: 0.7496 (ttt) cc_final: 0.7088 (ttt) REVERT: C 178 THR cc_start: 0.8637 (p) cc_final: 0.8305 (t) REVERT: D 147 MET cc_start: 0.7206 (ttt) cc_final: 0.6824 (ttt) REVERT: D 178 THR cc_start: 0.8450 (p) cc_final: 0.8079 (t) REVERT: E 147 MET cc_start: 0.3603 (ttt) cc_final: 0.3277 (ttt) REVERT: E 192 TYR cc_start: 0.6753 (m-80) cc_final: 0.6411 (m-80) REVERT: E 220 LEU cc_start: 0.8107 (tt) cc_final: 0.7870 (tp) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2122 time to fit residues: 59.4927 Evaluate side-chains 206 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS D 76 HIS ** E 76 HIS ** 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 = 0.4117 r_free = 0.4117 target = 0.159304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.134694 restraints weight = 11414.832| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.99 r_work: 0.3668 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9105 Z= 0.171 Angle : 0.549 7.848 12415 Z= 0.298 Chirality : 0.039 0.121 1410 Planarity : 0.004 0.035 1475 Dihedral : 4.057 35.635 1240 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.99 % Allowed : 13.26 % Favored : 84.75 % 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 aren not related in a simple way. whole: 2.35 (0.24), residues: 1100 helix: 1.81 (0.16), residues: 955 sheet: None (None), residues: 0 loop : 0.08 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 81 TYR 0.022 0.001 TYR B 111 PHE 0.021 0.002 PHE B 235 TRP 0.009 0.001 TRP B 160 HIS 0.010 0.005 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9105) covalent geometry : angle 0.54935 (12415) hydrogen bonds : bond 0.05581 ( 729) hydrogen bonds : angle 4.11781 ( 2187) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.192 Fit side-chains REVERT: A 147 MET cc_start: 0.7329 (ttt) cc_final: 0.6619 (ttt) REVERT: A 163 MET cc_start: 0.6962 (tpt) cc_final: 0.6657 (tpt) REVERT: A 220 LEU cc_start: 0.7894 (tt) cc_final: 0.7676 (tt) REVERT: B 86 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7397 (mt-10) REVERT: B 147 MET cc_start: 0.7569 (ttt) cc_final: 0.6888 (ttt) REVERT: C 77 TYR cc_start: 0.8430 (m-80) cc_final: 0.8091 (m-80) REVERT: C 147 MET cc_start: 0.7855 (ttt) cc_final: 0.7342 (ttt) REVERT: C 178 THR cc_start: 0.8602 (p) cc_final: 0.8351 (t) REVERT: C 187 TYR cc_start: 0.8332 (t80) cc_final: 0.8111 (t80) REVERT: C 206 PHE cc_start: 0.7970 (t80) cc_final: 0.7579 (t80) REVERT: C 228 ASP cc_start: 0.7600 (m-30) cc_final: 0.7269 (m-30) REVERT: D 92 THR cc_start: 0.7620 (t) cc_final: 0.7310 (p) REVERT: D 147 MET cc_start: 0.7594 (ttt) cc_final: 0.7135 (ttt) REVERT: D 162 TYR cc_start: 0.7378 (t80) cc_final: 0.7133 (t80) REVERT: D 163 MET cc_start: 0.7021 (tpt) cc_final: 0.6708 (tpt) REVERT: D 178 THR cc_start: 0.8517 (p) cc_final: 0.8241 (t) REVERT: E 147 MET cc_start: 0.3771 (ttt) cc_final: 0.3544 (ttt) outliers start: 18 outliers final: 6 residues processed: 220 average time/residue: 0.2234 time to fit residues: 55.2989 Evaluate side-chains 216 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 210 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 178 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 231 ASN B 76 HIS E 76 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.159455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.135430 restraints weight = 11622.155| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.96 r_work: 0.3658 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9105 Z= 0.142 Angle : 0.496 6.536 12415 Z= 0.265 Chirality : 0.037 0.116 1410 Planarity : 0.004 0.030 1475 Dihedral : 4.627 49.683 1240 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.32 % Allowed : 14.81 % Favored : 82.87 % 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 aren not related in a simple way. whole: 2.44 (0.24), residues: 1100 helix: 1.82 (0.16), residues: 960 sheet: None (None), residues: 0 loop : 0.44 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 81 TYR 0.019 0.001 TYR B 162 PHE 0.018 0.001 PHE E 235 TRP 0.007 0.001 TRP A 150 HIS 0.007 0.002 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9105) covalent geometry : angle 0.49618 (12415) hydrogen bonds : bond 0.04859 ( 729) hydrogen bonds : angle 3.71994 ( 2187) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.229 Fit side-chains REVERT: A 32 VAL cc_start: 0.8551 (t) cc_final: 0.8348 (m) REVERT: A 147 MET cc_start: 0.7077 (ttt) cc_final: 0.6428 (ttt) REVERT: A 163 MET cc_start: 0.7190 (tpt) cc_final: 0.6781 (tpt) REVERT: A 220 LEU cc_start: 0.7950 (tt) cc_final: 0.7747 (tp) REVERT: B 51 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7455 (mm-30) REVERT: B 83 VAL cc_start: 0.8693 (t) cc_final: 0.8418 (p) REVERT: B 147 MET cc_start: 0.7427 (ttt) cc_final: 0.6757 (ttt) REVERT: C 77 TYR cc_start: 0.8483 (m-80) cc_final: 0.8216 (m-80) REVERT: C 96 TYR cc_start: 0.8429 (m-80) cc_final: 0.8214 (m-80) REVERT: C 147 MET cc_start: 0.7826 (ttt) cc_final: 0.7325 (ttt) REVERT: C 178 THR cc_start: 0.8577 (p) cc_final: 0.8330 (t) REVERT: C 187 TYR cc_start: 0.8280 (t80) cc_final: 0.7985 (t80) REVERT: C 228 ASP cc_start: 0.7555 (m-30) cc_final: 0.7232 (m-30) REVERT: D 44 SER cc_start: 0.8647 (m) cc_final: 0.8424 (t) REVERT: D 92 THR cc_start: 0.7539 (t) cc_final: 0.7319 (p) REVERT: D 96 TYR cc_start: 0.8395 (m-80) cc_final: 0.8047 (m-80) REVERT: D 112 LEU cc_start: 0.7660 (mt) cc_final: 0.7366 (mm) REVERT: D 147 MET cc_start: 0.7521 (ttt) cc_final: 0.7059 (ttt) REVERT: D 162 TYR cc_start: 0.7382 (t80) cc_final: 0.7118 (t80) REVERT: D 163 MET cc_start: 0.7193 (tpt) cc_final: 0.6907 (tpt) REVERT: E 80 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7393 (mtm) REVERT: E 83 VAL cc_start: 0.8762 (t) cc_final: 0.8513 (p) REVERT: E 100 LEU cc_start: 0.8059 (tm) cc_final: 0.7764 (tt) REVERT: E 147 MET cc_start: 0.3373 (ttt) cc_final: 0.3160 (ttt) REVERT: E 220 LEU cc_start: 0.8063 (tp) cc_final: 0.7850 (mt) outliers start: 21 outliers final: 8 residues processed: 219 average time/residue: 0.2448 time to fit residues: 59.7911 Evaluate side-chains 206 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 197 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 178 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 108 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.159328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.134871 restraints weight = 11735.098| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.99 r_work: 0.3659 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9105 Z= 0.136 Angle : 0.500 6.383 12415 Z= 0.264 Chirality : 0.037 0.113 1410 Planarity : 0.004 0.044 1475 Dihedral : 4.786 53.591 1240 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.32 % Allowed : 16.69 % Favored : 80.99 % 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 aren not related in a simple way. whole: 2.40 (0.24), residues: 1100 helix: 1.81 (0.16), residues: 960 sheet: None (None), residues: 0 loop : 0.36 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 81 TYR 0.019 0.001 TYR B 111 PHE 0.015 0.001 PHE B 74 TRP 0.008 0.001 TRP A 168 HIS 0.002 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9105) covalent geometry : angle 0.50035 (12415) hydrogen bonds : bond 0.04495 ( 729) hydrogen bonds : angle 3.50714 ( 2187) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.176 Fit side-chains REVERT: A 147 MET cc_start: 0.7099 (ttt) cc_final: 0.6440 (ttt) REVERT: A 162 TYR cc_start: 0.7380 (t80) cc_final: 0.7092 (t80) REVERT: A 163 MET cc_start: 0.7286 (tpt) cc_final: 0.6908 (tpt) REVERT: A 209 TYR cc_start: 0.7329 (m-80) cc_final: 0.7084 (m-80) REVERT: A 223 ILE cc_start: 0.8277 (mt) cc_final: 0.8048 (mm) REVERT: B 83 VAL cc_start: 0.8691 (t) cc_final: 0.8420 (p) REVERT: B 147 MET cc_start: 0.7471 (ttt) cc_final: 0.6761 (ttt) REVERT: C 96 TYR cc_start: 0.8459 (m-80) cc_final: 0.8252 (m-80) REVERT: C 147 MET cc_start: 0.7784 (ttt) cc_final: 0.7296 (ttt) REVERT: C 178 THR cc_start: 0.8655 (p) cc_final: 0.8396 (t) REVERT: C 228 ASP cc_start: 0.7608 (m-30) cc_final: 0.7357 (m-30) REVERT: D 44 SER cc_start: 0.8644 (m) cc_final: 0.8414 (t) REVERT: D 96 TYR cc_start: 0.8419 (m-80) cc_final: 0.8149 (m-80) REVERT: D 147 MET cc_start: 0.7523 (ttt) cc_final: 0.7051 (ttt) REVERT: D 163 MET cc_start: 0.7180 (tpt) cc_final: 0.6938 (tpt) REVERT: E 80 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7390 (mtm) REVERT: E 83 VAL cc_start: 0.8708 (t) cc_final: 0.8487 (p) REVERT: E 100 LEU cc_start: 0.8049 (tm) cc_final: 0.7792 (tt) REVERT: E 147 MET cc_start: 0.2975 (ttt) cc_final: 0.2732 (ttt) outliers start: 21 outliers final: 9 residues processed: 225 average time/residue: 0.2612 time to fit residues: 65.2031 Evaluate side-chains 222 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 80 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.159068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.134918 restraints weight = 11677.328| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.01 r_work: 0.3658 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9105 Z= 0.137 Angle : 0.501 7.454 12415 Z= 0.265 Chirality : 0.037 0.117 1410 Planarity : 0.004 0.049 1475 Dihedral : 4.980 59.418 1240 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.87 % Allowed : 17.68 % Favored : 79.45 % 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 aren not related in a simple way. whole: 2.49 (0.24), residues: 1100 helix: 1.86 (0.16), residues: 955 sheet: None (None), residues: 0 loop : 0.49 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 81 TYR 0.027 0.001 TYR D 162 PHE 0.015 0.001 PHE C 235 TRP 0.009 0.001 TRP C 168 HIS 0.001 0.000 HIS D 76 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9105) covalent geometry : angle 0.50129 (12415) hydrogen bonds : bond 0.04394 ( 729) hydrogen bonds : angle 3.41477 ( 2187) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.200 Fit side-chains REVERT: A 78 MET cc_start: 0.8600 (mmm) cc_final: 0.8382 (mmm) REVERT: A 147 MET cc_start: 0.7139 (ttt) cc_final: 0.6456 (ttt) REVERT: A 162 TYR cc_start: 0.7365 (t80) cc_final: 0.7079 (t80) REVERT: A 163 MET cc_start: 0.7327 (tpt) cc_final: 0.6938 (tpt) REVERT: A 209 TYR cc_start: 0.7378 (m-80) cc_final: 0.7169 (m-80) REVERT: A 220 LEU cc_start: 0.8114 (tp) cc_final: 0.7910 (tm) REVERT: A 223 ILE cc_start: 0.8299 (mt) cc_final: 0.8077 (mm) REVERT: B 83 VAL cc_start: 0.8693 (t) cc_final: 0.8428 (p) REVERT: B 147 MET cc_start: 0.7431 (ttt) cc_final: 0.6729 (ttt) REVERT: C 77 TYR cc_start: 0.8490 (m-80) cc_final: 0.8250 (m-80) REVERT: C 147 MET cc_start: 0.7813 (ttt) cc_final: 0.7325 (ttt) REVERT: C 228 ASP cc_start: 0.7625 (m-30) cc_final: 0.7316 (m-30) REVERT: D 96 TYR cc_start: 0.8422 (m-80) cc_final: 0.8161 (m-80) REVERT: D 147 MET cc_start: 0.7530 (ttt) cc_final: 0.7040 (ttt) REVERT: D 163 MET cc_start: 0.7162 (tpt) cc_final: 0.6920 (tpt) REVERT: E 80 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7370 (mtm) REVERT: E 83 VAL cc_start: 0.8704 (t) cc_final: 0.8486 (p) REVERT: E 100 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7848 (tt) REVERT: E 147 MET cc_start: 0.2912 (ttt) cc_final: 0.2681 (ttt) outliers start: 26 outliers final: 12 residues processed: 232 average time/residue: 0.2678 time to fit residues: 68.9267 Evaluate side-chains 232 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 50 optimal weight: 0.0670 chunk 43 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.160383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.135833 restraints weight = 11676.643| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.03 r_work: 0.3674 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9105 Z= 0.123 Angle : 0.509 8.597 12415 Z= 0.263 Chirality : 0.037 0.115 1410 Planarity : 0.004 0.055 1475 Dihedral : 5.074 59.498 1240 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.76 % Allowed : 19.34 % Favored : 77.90 % 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 aren not related in a simple way. whole: 2.55 (0.24), residues: 1100 helix: 1.93 (0.16), residues: 955 sheet: None (None), residues: 0 loop : 0.29 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 81 TYR 0.023 0.001 TYR D 111 PHE 0.015 0.001 PHE C 235 TRP 0.011 0.001 TRP E 168 HIS 0.002 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9105) covalent geometry : angle 0.50871 (12415) hydrogen bonds : bond 0.04164 ( 729) hydrogen bonds : angle 3.35688 ( 2187) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.207 Fit side-chains REVERT: A 76 HIS cc_start: 0.8403 (m90) cc_final: 0.8193 (m90) REVERT: A 77 TYR cc_start: 0.8518 (m-80) cc_final: 0.8299 (m-80) REVERT: A 78 MET cc_start: 0.8623 (mmm) cc_final: 0.8373 (mmm) REVERT: A 147 MET cc_start: 0.7072 (ttt) cc_final: 0.6407 (ttt) REVERT: A 162 TYR cc_start: 0.7350 (t80) cc_final: 0.7082 (t80) REVERT: A 163 MET cc_start: 0.7368 (tpt) cc_final: 0.6987 (tpt) REVERT: A 209 TYR cc_start: 0.7398 (m-80) cc_final: 0.7170 (m-80) REVERT: A 220 LEU cc_start: 0.8134 (tp) cc_final: 0.7926 (tm) REVERT: A 223 ILE cc_start: 0.8295 (mt) cc_final: 0.8072 (mm) REVERT: B 83 VAL cc_start: 0.8676 (t) cc_final: 0.8420 (p) REVERT: B 147 MET cc_start: 0.7331 (ttt) cc_final: 0.6683 (ttt) REVERT: C 96 TYR cc_start: 0.8385 (m-80) cc_final: 0.8184 (m-80) REVERT: C 147 MET cc_start: 0.7775 (ttt) cc_final: 0.7308 (ttt) REVERT: D 96 TYR cc_start: 0.8420 (m-80) cc_final: 0.8162 (m-80) REVERT: D 147 MET cc_start: 0.7572 (ttt) cc_final: 0.7055 (ttt) REVERT: D 163 MET cc_start: 0.7201 (tpt) cc_final: 0.6949 (tpt) REVERT: E 51 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7110 (tm-30) REVERT: E 80 MET cc_start: 0.7588 (mtm) cc_final: 0.7353 (mtm) REVERT: E 100 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7830 (tt) REVERT: E 147 MET cc_start: 0.2886 (ttt) cc_final: 0.2661 (ttt) REVERT: E 205 TYR cc_start: 0.7870 (t80) cc_final: 0.7611 (t80) outliers start: 25 outliers final: 15 residues processed: 232 average time/residue: 0.2417 time to fit residues: 62.4652 Evaluate side-chains 235 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 228 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.158229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.134199 restraints weight = 11677.496| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.01 r_work: 0.3652 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9105 Z= 0.155 Angle : 0.538 8.191 12415 Z= 0.278 Chirality : 0.038 0.130 1410 Planarity : 0.004 0.053 1475 Dihedral : 5.282 52.244 1240 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.20 % Allowed : 19.34 % Favored : 77.46 % 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 aren not related in a simple way. whole: 2.49 (0.24), residues: 1100 helix: 1.91 (0.16), residues: 955 sheet: None (None), residues: 0 loop : 0.04 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 81 TYR 0.023 0.001 TYR D 111 PHE 0.018 0.001 PHE C 235 TRP 0.010 0.001 TRP E 168 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9105) covalent geometry : angle 0.53780 (12415) hydrogen bonds : bond 0.04433 ( 729) hydrogen bonds : angle 3.34356 ( 2187) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.215 Fit side-chains REVERT: A 77 TYR cc_start: 0.8538 (m-80) cc_final: 0.8283 (m-80) REVERT: A 78 MET cc_start: 0.8663 (mmm) cc_final: 0.8408 (mmm) REVERT: A 100 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7793 (tt) REVERT: A 147 MET cc_start: 0.7111 (ttt) cc_final: 0.6436 (ttt) REVERT: A 162 TYR cc_start: 0.7403 (t80) cc_final: 0.7117 (t80) REVERT: A 163 MET cc_start: 0.7404 (tpt) cc_final: 0.6993 (tpt) REVERT: A 209 TYR cc_start: 0.7459 (m-80) cc_final: 0.7197 (m-80) REVERT: A 220 LEU cc_start: 0.8164 (tp) cc_final: 0.7945 (tm) REVERT: A 223 ILE cc_start: 0.8394 (mt) cc_final: 0.8180 (mm) REVERT: B 83 VAL cc_start: 0.8683 (t) cc_final: 0.8421 (p) REVERT: B 147 MET cc_start: 0.7315 (ttt) cc_final: 0.6663 (ttt) REVERT: C 147 MET cc_start: 0.7771 (ttt) cc_final: 0.7304 (ttt) REVERT: D 51 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7302 (mm-30) REVERT: D 147 MET cc_start: 0.7539 (ttt) cc_final: 0.7043 (ttt) REVERT: D 190 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7729 (mtm) REVERT: E 100 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7852 (tt) REVERT: E 147 MET cc_start: 0.2872 (ttt) cc_final: 0.2647 (ttt) REVERT: E 190 MET cc_start: 0.8159 (mtt) cc_final: 0.7758 (mtt) outliers start: 29 outliers final: 17 residues processed: 234 average time/residue: 0.2480 time to fit residues: 64.7406 Evaluate side-chains 234 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 81 optimal weight: 0.0270 chunk 7 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.159636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.135994 restraints weight = 11651.647| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.96 r_work: 0.3674 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9105 Z= 0.129 Angle : 0.558 9.097 12415 Z= 0.283 Chirality : 0.038 0.186 1410 Planarity : 0.004 0.057 1475 Dihedral : 5.159 52.236 1240 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.98 % Allowed : 20.55 % Favored : 76.46 % 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 aren not related in a simple way. whole: 2.56 (0.24), residues: 1100 helix: 1.98 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.09 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 81 TYR 0.023 0.001 TYR D 111 PHE 0.018 0.001 PHE C 235 TRP 0.011 0.001 TRP B 168 HIS 0.003 0.001 HIS E 76 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9105) covalent geometry : angle 0.55801 (12415) hydrogen bonds : bond 0.04096 ( 729) hydrogen bonds : angle 3.34150 ( 2187) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 0.186 Fit side-chains REVERT: A 78 MET cc_start: 0.8615 (mmm) cc_final: 0.8366 (mmm) REVERT: A 100 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7777 (tt) REVERT: A 147 MET cc_start: 0.7037 (ttt) cc_final: 0.6386 (ttt) REVERT: A 162 TYR cc_start: 0.7335 (t80) cc_final: 0.7096 (t80) REVERT: A 163 MET cc_start: 0.7385 (tpt) cc_final: 0.7017 (tpt) REVERT: A 209 TYR cc_start: 0.7430 (m-80) cc_final: 0.7184 (m-80) REVERT: A 220 LEU cc_start: 0.8155 (tp) cc_final: 0.7946 (tm) REVERT: A 223 ILE cc_start: 0.8385 (mt) cc_final: 0.8157 (mm) REVERT: B 83 VAL cc_start: 0.8661 (t) cc_final: 0.8416 (p) REVERT: B 147 MET cc_start: 0.7310 (ttt) cc_final: 0.6695 (ttt) REVERT: C 147 MET cc_start: 0.7752 (ttt) cc_final: 0.7297 (ttt) REVERT: D 51 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7232 (mm-30) REVERT: D 96 TYR cc_start: 0.8359 (m-80) cc_final: 0.7922 (m-80) REVERT: D 147 MET cc_start: 0.7573 (ttt) cc_final: 0.7082 (ttt) REVERT: D 190 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7633 (mtm) REVERT: E 51 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7069 (tm-30) REVERT: E 147 MET cc_start: 0.2862 (ttt) cc_final: 0.2642 (ttt) REVERT: E 190 MET cc_start: 0.8093 (mtt) cc_final: 0.7646 (mtt) outliers start: 27 outliers final: 15 residues processed: 231 average time/residue: 0.2501 time to fit residues: 64.2886 Evaluate side-chains 233 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 29 TYR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 14 optimal weight: 7.9990 chunk 41 optimal weight: 0.0670 chunk 76 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.160694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137705 restraints weight = 11766.593| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.96 r_work: 0.3680 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9105 Z= 0.139 Angle : 0.602 13.849 12415 Z= 0.298 Chirality : 0.038 0.203 1410 Planarity : 0.004 0.045 1475 Dihedral : 5.129 53.710 1240 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.54 % Allowed : 21.10 % Favored : 76.35 % 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 aren not related in a simple way. whole: 2.52 (0.24), residues: 1100 helix: 1.96 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.20 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 81 TYR 0.044 0.001 TYR E 201 PHE 0.016 0.001 PHE C 235 TRP 0.015 0.001 TRP B 168 HIS 0.003 0.001 HIS E 76 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9105) covalent geometry : angle 0.60154 (12415) hydrogen bonds : bond 0.04178 ( 729) hydrogen bonds : angle 3.38527 ( 2187) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.212 Fit side-chains REVERT: A 78 MET cc_start: 0.8619 (mmm) cc_final: 0.8350 (mmm) REVERT: A 100 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7788 (tt) REVERT: A 147 MET cc_start: 0.7082 (ttt) cc_final: 0.6410 (ttt) REVERT: A 162 TYR cc_start: 0.7351 (t80) cc_final: 0.7105 (t80) REVERT: A 163 MET cc_start: 0.7400 (tpt) cc_final: 0.7035 (tpt) REVERT: A 209 TYR cc_start: 0.7442 (m-80) cc_final: 0.7181 (m-80) REVERT: A 220 LEU cc_start: 0.8183 (tp) cc_final: 0.7976 (tm) REVERT: A 223 ILE cc_start: 0.8303 (mt) cc_final: 0.8077 (mm) REVERT: B 83 VAL cc_start: 0.8657 (t) cc_final: 0.8409 (p) REVERT: B 147 MET cc_start: 0.7334 (ttt) cc_final: 0.6732 (ttt) REVERT: B 167 LEU cc_start: 0.8150 (tp) cc_final: 0.7949 (tm) REVERT: C 147 MET cc_start: 0.7756 (ttt) cc_final: 0.7304 (ttt) REVERT: D 51 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7242 (mm-30) REVERT: D 147 MET cc_start: 0.7581 (ttt) cc_final: 0.7043 (ttt) REVERT: D 190 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7552 (mtm) REVERT: E 51 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7134 (tm-30) REVERT: E 129 LEU cc_start: 0.6329 (tt) cc_final: 0.6075 (tt) REVERT: E 147 MET cc_start: 0.2874 (ttt) cc_final: 0.2658 (ttt) REVERT: E 163 MET cc_start: 0.7288 (tpt) cc_final: 0.6913 (tpt) REVERT: E 190 MET cc_start: 0.8109 (mtt) cc_final: 0.7686 (mtt) outliers start: 23 outliers final: 17 residues processed: 233 average time/residue: 0.2589 time to fit residues: 67.1701 Evaluate side-chains 238 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 29 TYR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain E residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 0.0870 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.161503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.137739 restraints weight = 11731.438| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.05 r_work: 0.3678 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9105 Z= 0.135 Angle : 0.617 13.865 12415 Z= 0.305 Chirality : 0.039 0.232 1410 Planarity : 0.004 0.045 1475 Dihedral : 5.237 54.211 1240 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.43 % Allowed : 20.99 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.53 (0.25), residues: 1100 helix: 1.98 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.26 (0.46), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 81 TYR 0.023 0.001 TYR D 111 PHE 0.017 0.001 PHE A 110 TRP 0.013 0.001 TRP B 168 HIS 0.001 0.000 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9105) covalent geometry : angle 0.61691 (12415) hydrogen bonds : bond 0.04128 ( 729) hydrogen bonds : angle 3.41827 ( 2187) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 0.318 Fit side-chains REVERT: A 78 MET cc_start: 0.8650 (mmm) cc_final: 0.8365 (mmm) REVERT: A 100 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7844 (tt) REVERT: A 147 MET cc_start: 0.7047 (ttt) cc_final: 0.6410 (ttt) REVERT: A 162 TYR cc_start: 0.7327 (t80) cc_final: 0.7106 (t80) REVERT: A 163 MET cc_start: 0.7427 (tpt) cc_final: 0.6962 (tpt) REVERT: A 209 TYR cc_start: 0.7436 (m-80) cc_final: 0.7175 (m-80) REVERT: A 220 LEU cc_start: 0.8173 (tp) cc_final: 0.7958 (tm) REVERT: A 223 ILE cc_start: 0.8291 (mt) cc_final: 0.8062 (mm) REVERT: B 83 VAL cc_start: 0.8648 (t) cc_final: 0.8394 (p) REVERT: B 140 TYR cc_start: 0.7661 (t80) cc_final: 0.7427 (t80) REVERT: B 147 MET cc_start: 0.7272 (ttt) cc_final: 0.6707 (ttt) REVERT: B 162 TYR cc_start: 0.7389 (t80) cc_final: 0.7138 (t80) REVERT: C 147 MET cc_start: 0.7757 (ttt) cc_final: 0.7273 (ttt) REVERT: D 51 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7269 (mm-30) REVERT: D 96 TYR cc_start: 0.8392 (m-80) cc_final: 0.8062 (m-80) REVERT: D 147 MET cc_start: 0.7563 (ttt) cc_final: 0.6986 (ttt) REVERT: D 190 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7493 (mtm) REVERT: D 231 ASN cc_start: 0.8190 (t0) cc_final: 0.7913 (m-40) REVERT: E 51 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7153 (tm-30) REVERT: E 129 LEU cc_start: 0.6401 (tt) cc_final: 0.6151 (tt) REVERT: E 147 MET cc_start: 0.2845 (ttt) cc_final: 0.2620 (ttt) REVERT: E 163 MET cc_start: 0.7305 (tpt) cc_final: 0.6913 (tpt) REVERT: E 190 MET cc_start: 0.8139 (mtt) cc_final: 0.7783 (mtt) outliers start: 22 outliers final: 17 residues processed: 232 average time/residue: 0.3460 time to fit residues: 89.0049 Evaluate side-chains 240 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 221 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 29 TYR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain E residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.161508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.138061 restraints weight = 11597.787| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.98 r_work: 0.3688 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9105 Z= 0.142 Angle : 0.630 14.325 12415 Z= 0.312 Chirality : 0.039 0.245 1410 Planarity : 0.004 0.050 1475 Dihedral : 5.210 52.243 1240 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.32 % Allowed : 21.10 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.24), residues: 1100 helix: 1.97 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.38 (0.45), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 81 TYR 0.023 0.001 TYR D 111 PHE 0.016 0.001 PHE C 235 TRP 0.014 0.001 TRP B 168 HIS 0.002 0.001 HIS E 76 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9105) covalent geometry : angle 0.63025 (12415) hydrogen bonds : bond 0.04193 ( 729) hydrogen bonds : angle 3.43295 ( 2187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.18 seconds wall clock time: 39 minutes 21.73 seconds (2361.73 seconds total)