Starting phenix.real_space_refine on Thu Mar 13 03:55:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cnk_16759/03_2025/8cnk_16759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cnk_16759/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cnk_16759/03_2025/8cnk_16759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cnk_16759/03_2025/8cnk_16759.map" model { file = "/net/cci-nas-00/data/ceres_data/8cnk_16759/03_2025/8cnk_16759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cnk_16759/03_2025/8cnk_16759.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.41, per 1000 atoms: 0.50 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: 1.92 Conformation dependent library (CDL) restraints added in 819.6 milliseconds 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: 0.84 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: 3.01 Time building geometry restraints manager: 2.22 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 20.340 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- 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= 0.290 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP B 75 HIS 0.000 0.000 HIS B 76 PHE 0.037 0.002 PHE E 94 TYR 0.006 0.001 TYR E 192 ARG 0.004 0.001 ARG A 52 *********************** 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 : 0.764 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: 0.7811 (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: 0.7883 (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: 0.6412 (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: 0.6241 time to fit residues: 174.9585 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 : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 56 optimal weight: 0.0030 chunk 44 optimal weight: 8.9990 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS D 76 HIS E 76 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.160281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.136166 restraints weight = 11435.609| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.94 r_work: 0.3670 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2123 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= 0.176 Angle : 0.536 7.779 12415 Z= 0.289 Chirality : 0.037 0.118 1410 Planarity : 0.004 0.031 1475 Dihedral : 3.971 31.566 1240 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.88 % Allowed : 13.26 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.25), residues: 1100 helix: 1.88 (0.16), residues: 955 sheet: None (None), residues: 0 loop : 0.08 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 160 HIS 0.010 0.005 HIS A 76 PHE 0.017 0.001 PHE C 235 TYR 0.021 0.001 TYR D 111 ARG 0.005 0.001 ARG B 81 *********************** 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 242 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 0.929 Fit side-chains REVERT: A 96 TYR cc_start: 0.8184 (m-80) cc_final: 0.7983 (m-80) REVERT: A 147 MET cc_start: 0.7239 (ttt) cc_final: 0.6542 (ttt) REVERT: A 163 MET cc_start: 0.6905 (tpt) cc_final: 0.6587 (tpt) REVERT: A 220 LEU cc_start: 0.7802 (tt) cc_final: 0.7596 (tt) REVERT: B 147 MET cc_start: 0.7514 (ttt) cc_final: 0.6857 (ttt) REVERT: C 147 MET cc_start: 0.7833 (ttt) cc_final: 0.7317 (ttt) REVERT: C 178 THR cc_start: 0.8569 (p) cc_final: 0.8337 (t) REVERT: C 187 TYR cc_start: 0.8280 (t80) cc_final: 0.8005 (t80) REVERT: C 206 PHE cc_start: 0.7999 (t80) cc_final: 0.7601 (t80) REVERT: D 92 THR cc_start: 0.7574 (t) cc_final: 0.7287 (p) REVERT: D 147 MET cc_start: 0.7586 (ttt) cc_final: 0.7131 (ttt) REVERT: D 163 MET cc_start: 0.6981 (tpt) cc_final: 0.6679 (tpt) REVERT: D 178 THR cc_start: 0.8458 (p) cc_final: 0.8199 (t) REVERT: E 147 MET cc_start: 0.3787 (ttt) cc_final: 0.3534 (ttt) outliers start: 17 outliers final: 6 residues processed: 229 average time/residue: 0.6514 time to fit residues: 167.8976 Evaluate side-chains 211 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 205 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.159885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.135748 restraints weight = 11604.333| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.96 r_work: 0.3666 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2580 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= 0.189 Angle : 0.500 5.930 12415 Z= 0.267 Chirality : 0.037 0.114 1410 Planarity : 0.004 0.029 1475 Dihedral : 4.523 46.584 1240 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.21 % Allowed : 16.13 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.24), residues: 1100 helix: 1.84 (0.16), residues: 960 sheet: None (None), residues: 0 loop : 0.42 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 150 HIS 0.007 0.001 HIS A 76 PHE 0.020 0.001 PHE B 235 TYR 0.019 0.001 TYR B 111 ARG 0.003 0.001 ARG E 54 *********************** 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 234 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.920 Fit side-chains REVERT: A 32 VAL cc_start: 0.8651 (t) cc_final: 0.8424 (m) REVERT: A 147 MET cc_start: 0.7100 (ttt) cc_final: 0.6463 (ttt) REVERT: A 163 MET cc_start: 0.7222 (tpt) cc_final: 0.6788 (tpt) REVERT: A 220 LEU cc_start: 0.7950 (tt) cc_final: 0.7731 (tt) REVERT: B 83 VAL cc_start: 0.8693 (t) cc_final: 0.8419 (p) REVERT: B 147 MET cc_start: 0.7392 (ttt) cc_final: 0.6752 (ttt) REVERT: B 191 MET cc_start: 0.8144 (ttt) cc_final: 0.7934 (tpp) REVERT: C 77 TYR cc_start: 0.8494 (m-80) cc_final: 0.8195 (m-80) REVERT: C 96 TYR cc_start: 0.8425 (m-80) cc_final: 0.8219 (m-80) REVERT: C 147 MET cc_start: 0.7807 (ttt) cc_final: 0.7317 (ttt) REVERT: C 178 THR cc_start: 0.8630 (p) cc_final: 0.8363 (t) REVERT: C 187 TYR cc_start: 0.8282 (t80) cc_final: 0.7983 (t80) REVERT: C 228 ASP cc_start: 0.7496 (m-30) cc_final: 0.7172 (m-30) REVERT: D 44 SER cc_start: 0.8692 (m) cc_final: 0.8469 (t) REVERT: D 92 THR cc_start: 0.7532 (t) cc_final: 0.7287 (p) REVERT: D 96 TYR cc_start: 0.8393 (m-80) cc_final: 0.8043 (m-80) REVERT: D 147 MET cc_start: 0.7541 (ttt) cc_final: 0.7076 (ttt) REVERT: D 163 MET cc_start: 0.7168 (tpt) cc_final: 0.6895 (tpt) REVERT: E 83 VAL cc_start: 0.8760 (t) cc_final: 0.8506 (p) REVERT: E 100 LEU cc_start: 0.8072 (tm) cc_final: 0.7772 (tt) REVERT: E 147 MET cc_start: 0.3276 (ttt) cc_final: 0.3044 (ttt) REVERT: E 205 TYR cc_start: 0.7704 (t80) cc_final: 0.7374 (t80) outliers start: 20 outliers final: 9 residues processed: 219 average time/residue: 0.7089 time to fit residues: 172.1638 Evaluate side-chains 208 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 199 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 163 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 248 SER 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 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 12 optimal weight: 0.0050 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.160127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.135985 restraints weight = 11563.322| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.96 r_work: 0.3674 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9105 Z= 0.179 Angle : 0.496 7.523 12415 Z= 0.261 Chirality : 0.037 0.113 1410 Planarity : 0.004 0.044 1475 Dihedral : 4.668 51.520 1240 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.54 % Allowed : 17.24 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.24), residues: 1100 helix: 1.86 (0.16), residues: 960 sheet: None (None), residues: 0 loop : 0.44 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 168 HIS 0.008 0.001 HIS A 76 PHE 0.016 0.001 PHE B 235 TYR 0.018 0.001 TYR B 111 ARG 0.005 0.001 ARG B 81 *********************** 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 247 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.811 Fit side-chains REVERT: A 147 MET cc_start: 0.7133 (ttt) cc_final: 0.6472 (ttt) REVERT: A 162 TYR cc_start: 0.7416 (t80) cc_final: 0.7138 (t80) REVERT: A 220 LEU cc_start: 0.7978 (tt) cc_final: 0.7766 (tt) REVERT: B 83 VAL cc_start: 0.8681 (t) cc_final: 0.8425 (p) REVERT: B 147 MET cc_start: 0.7412 (ttt) cc_final: 0.6736 (ttt) REVERT: C 77 TYR cc_start: 0.8524 (m-80) cc_final: 0.8291 (m-80) REVERT: C 96 TYR cc_start: 0.8465 (m-80) cc_final: 0.8257 (m-80) REVERT: C 147 MET cc_start: 0.7749 (ttt) cc_final: 0.7291 (ttt) REVERT: C 228 ASP cc_start: 0.7551 (m-30) cc_final: 0.7272 (m-30) REVERT: D 44 SER cc_start: 0.8652 (m) cc_final: 0.8428 (t) REVERT: D 96 TYR cc_start: 0.8422 (m-80) cc_final: 0.8139 (m-80) REVERT: D 112 LEU cc_start: 0.7748 (mt) cc_final: 0.7439 (mm) REVERT: D 147 MET cc_start: 0.7515 (ttt) cc_final: 0.7050 (ttt) REVERT: D 163 MET cc_start: 0.7187 (tpt) cc_final: 0.6941 (tpt) REVERT: E 70 THR cc_start: 0.8611 (m) cc_final: 0.8411 (m) REVERT: E 83 VAL cc_start: 0.8724 (t) cc_final: 0.8490 (p) REVERT: E 100 LEU cc_start: 0.8114 (tm) cc_final: 0.7855 (tt) REVERT: E 147 MET cc_start: 0.3198 (ttt) cc_final: 0.2967 (ttt) outliers start: 23 outliers final: 8 residues processed: 234 average time/residue: 0.6767 time to fit residues: 175.9367 Evaluate side-chains 227 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 163 MET Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 80 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.159786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.135626 restraints weight = 11592.203| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.96 r_work: 0.3669 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9105 Z= 0.187 Angle : 0.502 7.823 12415 Z= 0.262 Chirality : 0.037 0.126 1410 Planarity : 0.004 0.043 1475 Dihedral : 4.980 58.046 1240 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 3.20 % Allowed : 18.78 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.24), residues: 1100 helix: 1.93 (0.16), residues: 955 sheet: None (None), residues: 0 loop : 0.55 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 168 HIS 0.001 0.000 HIS A 76 PHE 0.015 0.001 PHE B 235 TYR 0.022 0.001 TYR D 111 ARG 0.005 0.001 ARG D 81 *********************** 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 253 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.806 Fit side-chains REVERT: A 141 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7573 (mtt) REVERT: A 147 MET cc_start: 0.7085 (ttt) cc_final: 0.6417 (ttt) REVERT: A 162 TYR cc_start: 0.7379 (t80) cc_final: 0.7107 (t80) REVERT: A 209 TYR cc_start: 0.7313 (m-80) cc_final: 0.7104 (m-80) REVERT: A 223 ILE cc_start: 0.8266 (mt) cc_final: 0.8035 (mm) REVERT: B 83 VAL cc_start: 0.8675 (t) cc_final: 0.8423 (p) REVERT: B 147 MET cc_start: 0.7392 (ttt) cc_final: 0.6720 (ttt) REVERT: C 77 TYR cc_start: 0.8540 (m-80) cc_final: 0.8326 (m-80) REVERT: C 147 MET cc_start: 0.7753 (ttt) cc_final: 0.7301 (ttt) REVERT: C 228 ASP cc_start: 0.7610 (m-30) cc_final: 0.7332 (m-30) REVERT: D 44 SER cc_start: 0.8653 (m) cc_final: 0.8404 (t) REVERT: D 96 TYR cc_start: 0.8421 (m-80) cc_final: 0.8141 (m-80) REVERT: D 147 MET cc_start: 0.7505 (ttt) cc_final: 0.7034 (ttt) REVERT: D 163 MET cc_start: 0.7185 (tpt) cc_final: 0.6917 (tpt) REVERT: E 70 THR cc_start: 0.8636 (m) cc_final: 0.8414 (m) REVERT: E 83 VAL cc_start: 0.8678 (t) cc_final: 0.8471 (p) REVERT: E 100 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7876 (tt) REVERT: E 147 MET cc_start: 0.2899 (ttt) cc_final: 0.2666 (ttt) outliers start: 29 outliers final: 13 residues processed: 235 average time/residue: 0.6696 time to fit residues: 175.5284 Evaluate side-chains 235 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 220 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 66 SER 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 32 VAL 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 100 LEU Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4109 r_free = 0.4109 target = 0.159431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.135348 restraints weight = 11576.861| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.00 r_work: 0.3667 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9105 Z= 0.180 Angle : 0.514 10.445 12415 Z= 0.265 Chirality : 0.037 0.137 1410 Planarity : 0.004 0.041 1475 Dihedral : 4.980 58.168 1240 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.09 % Allowed : 19.23 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.24), residues: 1100 helix: 2.00 (0.16), residues: 955 sheet: None (None), residues: 0 loop : 0.29 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 168 HIS 0.001 0.000 HIS C 76 PHE 0.015 0.001 PHE D 235 TYR 0.025 0.001 TYR D 111 ARG 0.006 0.001 ARG D 81 *********************** 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 248 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.803 Fit side-chains REVERT: A 141 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7661 (mtt) REVERT: A 147 MET cc_start: 0.7054 (ttt) cc_final: 0.6397 (ttt) REVERT: A 162 TYR cc_start: 0.7375 (t80) cc_final: 0.7114 (t80) REVERT: A 209 TYR cc_start: 0.7308 (m-80) cc_final: 0.7106 (m-80) REVERT: A 223 ILE cc_start: 0.8270 (mt) cc_final: 0.8040 (mm) REVERT: B 83 VAL cc_start: 0.8667 (t) cc_final: 0.8425 (p) REVERT: B 147 MET cc_start: 0.7354 (ttt) cc_final: 0.6700 (ttt) REVERT: C 147 MET cc_start: 0.7789 (ttt) cc_final: 0.7316 (ttt) REVERT: D 96 TYR cc_start: 0.8412 (m-80) cc_final: 0.8151 (m-80) REVERT: D 147 MET cc_start: 0.7512 (ttt) cc_final: 0.7021 (ttt) REVERT: D 163 MET cc_start: 0.7233 (tpt) cc_final: 0.6945 (tpt) REVERT: E 51 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7091 (tm-30) REVERT: E 70 THR cc_start: 0.8664 (m) cc_final: 0.8422 (m) REVERT: E 147 MET cc_start: 0.2869 (ttt) cc_final: 0.2637 (ttt) outliers start: 28 outliers final: 16 residues processed: 233 average time/residue: 0.6580 time to fit residues: 170.8134 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 : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 163 MET 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 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 220 LEU 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 E residue 220 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 78 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.159696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.135518 restraints weight = 11624.475| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.01 r_work: 0.3668 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9105 Z= 0.182 Angle : 0.529 9.392 12415 Z= 0.269 Chirality : 0.037 0.134 1410 Planarity : 0.004 0.040 1475 Dihedral : 5.018 56.441 1240 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.31 % Allowed : 19.67 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.24), residues: 1100 helix: 2.05 (0.16), residues: 955 sheet: None (None), residues: 0 loop : 0.12 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 168 HIS 0.001 0.000 HIS A 76 PHE 0.017 0.001 PHE C 235 TYR 0.023 0.001 TYR D 111 ARG 0.006 0.001 ARG D 81 *********************** 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 245 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.891 Fit side-chains REVERT: A 100 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7723 (tt) REVERT: A 141 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7607 (mtt) REVERT: A 147 MET cc_start: 0.7079 (ttt) cc_final: 0.6411 (ttt) REVERT: A 162 TYR cc_start: 0.7374 (t80) cc_final: 0.7128 (t80) REVERT: A 223 ILE cc_start: 0.8260 (mt) cc_final: 0.8032 (mm) REVERT: B 83 VAL cc_start: 0.8665 (t) cc_final: 0.8423 (p) REVERT: B 147 MET cc_start: 0.7312 (ttt) cc_final: 0.6707 (ttt) REVERT: C 147 MET cc_start: 0.7761 (ttt) cc_final: 0.7295 (ttt) REVERT: D 51 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7283 (mm-30) REVERT: D 147 MET cc_start: 0.7467 (ttt) cc_final: 0.6985 (ttt) REVERT: D 163 MET cc_start: 0.7265 (tpt) cc_final: 0.6977 (tpt) REVERT: E 51 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7107 (tm-30) REVERT: E 70 THR cc_start: 0.8660 (m) cc_final: 0.8445 (m) REVERT: E 112 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7804 (mp) REVERT: E 147 MET cc_start: 0.2850 (ttt) cc_final: 0.2610 (ttt) REVERT: E 190 MET cc_start: 0.8215 (mtt) cc_final: 0.7873 (mtt) REVERT: E 205 TYR cc_start: 0.7800 (t80) cc_final: 0.7487 (t80) outliers start: 30 outliers final: 19 residues processed: 229 average time/residue: 0.6769 time to fit residues: 172.5947 Evaluate side-chains 235 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 141 MET Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 163 MET 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 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 180 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 chunk 90 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.160411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.135986 restraints weight = 11831.052| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.05 r_work: 0.3674 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3673 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= 0.169 Angle : 0.537 9.586 12415 Z= 0.272 Chirality : 0.037 0.162 1410 Planarity : 0.004 0.034 1475 Dihedral : 4.955 55.458 1240 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.87 % Allowed : 19.78 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.24), residues: 1100 helix: 2.09 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.01 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 168 HIS 0.002 0.001 HIS A 76 PHE 0.018 0.001 PHE C 235 TYR 0.023 0.001 TYR D 111 ARG 0.006 0.001 ARG D 81 *********************** 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 243 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.804 Fit side-chains REVERT: A 100 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7807 (tt) REVERT: A 141 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7629 (mtt) REVERT: A 147 MET cc_start: 0.7031 (ttt) cc_final: 0.6383 (ttt) REVERT: A 162 TYR cc_start: 0.7330 (t80) cc_final: 0.7103 (t80) REVERT: A 223 ILE cc_start: 0.8368 (mt) cc_final: 0.8148 (mm) REVERT: B 83 VAL cc_start: 0.8654 (t) cc_final: 0.8422 (p) REVERT: B 147 MET cc_start: 0.7310 (ttt) cc_final: 0.6711 (ttt) REVERT: C 147 MET cc_start: 0.7759 (ttt) cc_final: 0.7276 (ttt) REVERT: D 51 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7259 (mm-30) REVERT: D 96 TYR cc_start: 0.8361 (m-80) cc_final: 0.8078 (m-80) REVERT: D 147 MET cc_start: 0.7437 (ttt) cc_final: 0.6958 (ttt) REVERT: D 163 MET cc_start: 0.7229 (tpt) cc_final: 0.6954 (tpt) REVERT: E 70 THR cc_start: 0.8675 (m) cc_final: 0.8445 (m) REVERT: E 147 MET cc_start: 0.2764 (ttt) cc_final: 0.2529 (ttt) REVERT: E 190 MET cc_start: 0.8212 (mtt) cc_final: 0.7806 (mtt) REVERT: E 205 TYR cc_start: 0.7793 (t80) cc_final: 0.7490 (t80) outliers start: 26 outliers final: 16 residues processed: 230 average time/residue: 0.6597 time to fit residues: 168.8750 Evaluate side-chains 232 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 141 MET Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 163 MET 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 C residue 248 SER Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 113 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 94 optimal weight: 0.0980 chunk 30 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.160862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.136442 restraints weight = 11639.833| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.04 r_work: 0.3680 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9105 Z= 0.169 Angle : 0.578 10.847 12415 Z= 0.288 Chirality : 0.038 0.209 1410 Planarity : 0.004 0.051 1475 Dihedral : 4.912 53.819 1240 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.98 % Allowed : 20.33 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.24), residues: 1100 helix: 2.11 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.10 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 168 HIS 0.002 0.001 HIS E 76 PHE 0.016 0.001 PHE C 235 TYR 0.024 0.001 TYR D 111 ARG 0.008 0.001 ARG B 81 *********************** 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 249 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 0.957 Fit side-chains REVERT: A 100 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7796 (tt) REVERT: A 141 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7610 (mtt) REVERT: A 147 MET cc_start: 0.7029 (ttt) cc_final: 0.6420 (ttt) REVERT: A 162 TYR cc_start: 0.7288 (t80) cc_final: 0.7055 (t80) REVERT: A 223 ILE cc_start: 0.8281 (mt) cc_final: 0.8046 (mm) REVERT: B 83 VAL cc_start: 0.8644 (t) cc_final: 0.8433 (p) REVERT: B 147 MET cc_start: 0.7280 (ttt) cc_final: 0.6684 (ttt) REVERT: C 147 MET cc_start: 0.7710 (ttt) cc_final: 0.7229 (ttt) REVERT: D 51 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7242 (mm-30) REVERT: D 147 MET cc_start: 0.7434 (ttt) cc_final: 0.6904 (ttt) REVERT: D 163 MET cc_start: 0.7232 (tpt) cc_final: 0.6949 (tpt) REVERT: E 51 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7127 (tm-30) REVERT: E 70 THR cc_start: 0.8646 (m) cc_final: 0.8388 (m) REVERT: E 147 MET cc_start: 0.2813 (ttt) cc_final: 0.2572 (ttt) REVERT: E 163 MET cc_start: 0.7264 (tpt) cc_final: 0.6924 (tpt) REVERT: E 190 MET cc_start: 0.8161 (mtt) cc_final: 0.7726 (mtt) REVERT: E 205 TYR cc_start: 0.7749 (t80) cc_final: 0.7522 (t80) outliers start: 27 outliers final: 17 residues processed: 233 average time/residue: 0.6773 time to fit residues: 175.6484 Evaluate side-chains 236 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 141 MET Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 42 LEU 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 220 LEU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 113 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 0.0370 chunk 87 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.161434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137293 restraints weight = 11667.845| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.04 r_work: 0.3692 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3926 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= 0.166 Angle : 0.606 15.412 12415 Z= 0.298 Chirality : 0.038 0.237 1410 Planarity : 0.004 0.044 1475 Dihedral : 4.823 52.822 1240 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.43 % Allowed : 21.55 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.24), residues: 1100 helix: 2.14 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.22 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 168 HIS 0.001 0.000 HIS A 76 PHE 0.015 0.001 PHE C 235 TYR 0.028 0.001 TYR D 96 ARG 0.006 0.001 ARG B 81 ********************** 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 245 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.939 Fit side-chains REVERT: A 100 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7804 (tt) REVERT: A 141 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7604 (mtt) REVERT: A 147 MET cc_start: 0.7033 (ttt) cc_final: 0.6420 (ttt) REVERT: A 162 TYR cc_start: 0.7285 (t80) cc_final: 0.7068 (t80) REVERT: A 223 ILE cc_start: 0.8321 (mt) cc_final: 0.8088 (mm) REVERT: B 83 VAL cc_start: 0.8625 (t) cc_final: 0.8404 (p) REVERT: B 147 MET cc_start: 0.7191 (ttt) cc_final: 0.6647 (ttt) REVERT: B 189 THR cc_start: 0.8214 (t) cc_final: 0.7836 (p) REVERT: C 147 MET cc_start: 0.7722 (ttt) cc_final: 0.7244 (ttt) REVERT: D 51 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7214 (mm-30) REVERT: D 83 VAL cc_start: 0.8737 (t) cc_final: 0.8437 (p) REVERT: D 147 MET cc_start: 0.7488 (ttt) cc_final: 0.6971 (ttt) REVERT: D 163 MET cc_start: 0.7219 (tpt) cc_final: 0.6951 (tpt) REVERT: E 51 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7135 (tm-30) REVERT: E 70 THR cc_start: 0.8607 (m) cc_final: 0.8364 (m) REVERT: E 129 LEU cc_start: 0.6384 (tt) cc_final: 0.6158 (tt) REVERT: E 147 MET cc_start: 0.2762 (ttt) cc_final: 0.2518 (ttt) REVERT: E 163 MET cc_start: 0.7256 (tpt) cc_final: 0.6923 (tpt) outliers start: 22 outliers final: 15 residues processed: 234 average time/residue: 0.6430 time to fit residues: 167.8541 Evaluate side-chains 235 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 141 MET Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 163 MET 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 220 LEU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 113 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 0.0470 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.158878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.135356 restraints weight = 11706.002| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.99 r_work: 0.3673 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9105 Z= 0.247 Angle : 0.649 13.916 12415 Z= 0.321 Chirality : 0.041 0.245 1410 Planarity : 0.004 0.050 1475 Dihedral : 5.078 58.292 1240 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.43 % Allowed : 21.44 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.24), residues: 1100 helix: 2.00 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.31 (0.46), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 168 HIS 0.001 0.000 HIS A 76 PHE 0.018 0.002 PHE C 235 TYR 0.029 0.001 TYR E 201 ARG 0.007 0.001 ARG B 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5924.27 seconds wall clock time: 101 minutes 52.06 seconds (6112.06 seconds total)