Starting phenix.real_space_refine on Fri Nov 15 08:07:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cnk_16759/11_2024/8cnk_16759.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cnk_16759/11_2024/8cnk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cnk_16759/11_2024/8cnk_16759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cnk_16759/11_2024/8cnk_16759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cnk_16759/11_2024/8cnk_16759.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cnk_16759/11_2024/8cnk_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-5513/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: 5.45, per 1000 atoms: 0.62 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: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.59 Time building geometry restraints manager: 2.83 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: 0.00 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: 0.320 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.210 Find NCS groups from input model: 0.330 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:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- 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 : 0.908 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: 0.6140 time to fit residues: 172.2957 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 : 0.963 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 0.900 Fit side-chains REVERT: A 147 MET cc_start: 0.6850 (ttt) cc_final: 0.6301 (ttt) REVERT: A 220 LEU cc_start: 0.7808 (tt) cc_final: 0.7580 (tt) REVERT: B 147 MET cc_start: 0.7127 (ttt) cc_final: 0.6617 (ttt) REVERT: C 69 VAL cc_start: 0.8476 (t) cc_final: 0.8259 (t) REVERT: C 147 MET cc_start: 0.7468 (ttt) cc_final: 0.7107 (ttt) REVERT: C 178 THR cc_start: 0.8550 (p) cc_final: 0.8287 (t) REVERT: C 187 TYR cc_start: 0.7883 (t80) cc_final: 0.7668 (t80) REVERT: C 206 PHE cc_start: 0.7353 (t80) cc_final: 0.7003 (t80) REVERT: D 69 VAL cc_start: 0.8248 (t) cc_final: 0.8043 (t) REVERT: D 92 THR cc_start: 0.7261 (t) cc_final: 0.6983 (p) REVERT: D 112 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7379 (mt) REVERT: D 147 MET cc_start: 0.7125 (ttt) cc_final: 0.6810 (ttt) REVERT: D 163 MET cc_start: 0.6481 (tpt) cc_final: 0.6278 (tpt) REVERT: D 178 THR cc_start: 0.8457 (p) cc_final: 0.8180 (t) REVERT: E 147 MET cc_start: 0.3554 (ttt) cc_final: 0.3329 (ttt) REVERT: E 220 LEU cc_start: 0.7928 (tt) cc_final: 0.7722 (tp) outliers start: 17 outliers final: 6 residues processed: 229 average time/residue: 0.6606 time to fit residues: 169.6505 Evaluate side-chains 211 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 204 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 112 LEU 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 55 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 0.0070 chunk 80 optimal weight: 4.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9105 Z= 0.286 Angle : 0.540 5.731 12415 Z= 0.291 Chirality : 0.039 0.120 1410 Planarity : 0.004 0.032 1475 Dihedral : 4.929 52.182 1240 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.54 % Allowed : 16.91 % Favored : 80.55 % 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: 2.43 (0.24), residues: 1100 helix: 1.77 (0.16), residues: 955 sheet: None (None), residues: 0 loop : 0.85 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 75 HIS 0.006 0.001 HIS A 76 PHE 0.023 0.002 PHE B 235 TYR 0.020 0.002 TYR B 111 ARG 0.004 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 246 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.964 Fit side-chains REVERT: A 147 MET cc_start: 0.6806 (ttt) cc_final: 0.6278 (ttt) REVERT: A 187 TYR cc_start: 0.7916 (t80) cc_final: 0.7713 (t80) REVERT: A 220 LEU cc_start: 0.7966 (tt) cc_final: 0.7741 (tt) REVERT: B 83 VAL cc_start: 0.8529 (t) cc_final: 0.8223 (p) REVERT: B 147 MET cc_start: 0.7189 (ttt) cc_final: 0.6613 (ttt) REVERT: B 220 LEU cc_start: 0.8021 (tt) cc_final: 0.7793 (tp) REVERT: C 77 TYR cc_start: 0.8160 (m-80) cc_final: 0.7845 (m-80) REVERT: C 147 MET cc_start: 0.7481 (ttt) cc_final: 0.7121 (ttt) REVERT: C 178 THR cc_start: 0.8650 (p) cc_final: 0.8317 (t) REVERT: C 228 ASP cc_start: 0.6811 (m-30) cc_final: 0.6466 (m-30) REVERT: D 92 THR cc_start: 0.7288 (t) cc_final: 0.7030 (p) REVERT: D 112 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7538 (mt) REVERT: D 147 MET cc_start: 0.7167 (ttt) cc_final: 0.6833 (ttt) REVERT: D 162 TYR cc_start: 0.7382 (t80) cc_final: 0.7144 (t80) REVERT: E 100 LEU cc_start: 0.7914 (tm) cc_final: 0.7647 (tt) REVERT: E 147 MET cc_start: 0.2958 (ttt) cc_final: 0.2751 (ttt) REVERT: E 220 LEU cc_start: 0.8100 (tt) cc_final: 0.7834 (tt) outliers start: 23 outliers final: 13 residues processed: 232 average time/residue: 0.6691 time to fit residues: 173.5074 Evaluate side-chains 222 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 B residue 180 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 66 SER 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 112 LEU 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 98 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.0980 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 0.0370 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9105 Z= 0.155 Angle : 0.495 7.629 12415 Z= 0.261 Chirality : 0.036 0.107 1410 Planarity : 0.004 0.049 1475 Dihedral : 4.908 53.601 1240 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.65 % Allowed : 18.56 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.59 (0.24), residues: 1100 helix: 1.90 (0.16), residues: 955 sheet: None (None), residues: 0 loop : 0.71 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 160 HIS 0.001 0.000 HIS A 76 PHE 0.014 0.001 PHE E 235 TYR 0.022 0.001 TYR B 162 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 246 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.931 Fit side-chains REVERT: A 147 MET cc_start: 0.6787 (ttt) cc_final: 0.6265 (ttt) REVERT: A 220 LEU cc_start: 0.7981 (tt) cc_final: 0.7744 (tt) REVERT: B 83 VAL cc_start: 0.8494 (t) cc_final: 0.8223 (p) REVERT: B 147 MET cc_start: 0.7141 (ttt) cc_final: 0.6573 (ttt) REVERT: B 220 LEU cc_start: 0.8022 (tt) cc_final: 0.7767 (tp) REVERT: C 77 TYR cc_start: 0.8197 (m-80) cc_final: 0.7963 (m-80) REVERT: C 147 MET cc_start: 0.7451 (ttt) cc_final: 0.7099 (ttt) REVERT: C 228 ASP cc_start: 0.6855 (m-30) cc_final: 0.6552 (m-30) REVERT: D 147 MET cc_start: 0.7141 (ttt) cc_final: 0.6793 (ttt) REVERT: E 83 VAL cc_start: 0.8491 (t) cc_final: 0.8260 (p) REVERT: E 100 LEU cc_start: 0.7903 (tm) cc_final: 0.7667 (tt) REVERT: E 147 MET cc_start: 0.2783 (ttt) cc_final: 0.2569 (ttt) REVERT: E 220 LEU cc_start: 0.8027 (tt) cc_final: 0.7761 (tt) outliers start: 24 outliers final: 5 residues processed: 232 average time/residue: 0.6930 time to fit residues: 178.9599 Evaluate side-chains 218 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 213 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 193 ILE Chi-restraints excluded: chain C residue 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9105 Z= 0.231 Angle : 0.518 7.911 12415 Z= 0.274 Chirality : 0.038 0.114 1410 Planarity : 0.004 0.047 1475 Dihedral : 5.297 59.271 1240 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.76 % Allowed : 19.34 % Favored : 76.91 % 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: 2.50 (0.24), residues: 1100 helix: 1.87 (0.16), residues: 955 sheet: None (None), residues: 0 loop : 0.41 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 168 HIS 0.001 0.001 HIS A 76 PHE 0.018 0.001 PHE C 235 TYR 0.022 0.001 TYR D 111 ARG 0.004 0.001 ARG E 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 258 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 1.066 Fit side-chains REVERT: A 147 MET cc_start: 0.6803 (ttt) cc_final: 0.6250 (ttt) REVERT: A 209 TYR cc_start: 0.6939 (m-80) cc_final: 0.6699 (m-80) REVERT: B 83 VAL cc_start: 0.8501 (t) cc_final: 0.8224 (p) REVERT: B 147 MET cc_start: 0.7160 (ttt) cc_final: 0.6586 (ttt) REVERT: B 220 LEU cc_start: 0.8116 (tt) cc_final: 0.7859 (tp) REVERT: C 147 MET cc_start: 0.7432 (ttt) cc_final: 0.7090 (ttt) REVERT: D 147 MET cc_start: 0.7128 (ttt) cc_final: 0.6767 (ttt) REVERT: E 83 VAL cc_start: 0.8494 (t) cc_final: 0.8254 (p) REVERT: E 100 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7706 (tt) REVERT: E 220 LEU cc_start: 0.8092 (tt) cc_final: 0.7827 (tt) outliers start: 34 outliers final: 17 residues processed: 240 average time/residue: 0.7117 time to fit residues: 190.4969 Evaluate side-chains 237 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 219 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 32 VAL 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 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 50 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 178 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 0.027 9105 Z= 0.217 Angle : 0.520 9.077 12415 Z= 0.271 Chirality : 0.038 0.111 1410 Planarity : 0.004 0.048 1475 Dihedral : 5.335 54.193 1240 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.76 % Allowed : 19.12 % Favored : 77.13 % 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: 2.49 (0.24), residues: 1100 helix: 1.90 (0.16), residues: 955 sheet: None (None), residues: 0 loop : 0.13 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 168 HIS 0.001 0.000 HIS C 76 PHE 0.018 0.001 PHE C 235 TYR 0.024 0.001 TYR A 162 ARG 0.006 0.001 ARG A 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 257 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 147 MET cc_start: 0.6780 (ttt) cc_final: 0.6245 (ttt) REVERT: A 220 LEU cc_start: 0.8120 (tp) cc_final: 0.7828 (tm) REVERT: B 83 VAL cc_start: 0.8497 (t) cc_final: 0.8220 (p) REVERT: B 147 MET cc_start: 0.7161 (ttt) cc_final: 0.6585 (ttt) REVERT: B 220 LEU cc_start: 0.8153 (tt) cc_final: 0.7880 (tp) REVERT: C 147 MET cc_start: 0.7412 (ttt) cc_final: 0.7074 (ttt) REVERT: D 96 TYR cc_start: 0.8280 (m-80) cc_final: 0.7942 (m-80) REVERT: D 147 MET cc_start: 0.7122 (ttt) cc_final: 0.6748 (ttt) REVERT: D 163 MET cc_start: 0.6515 (tpp) cc_final: 0.6273 (tpp) REVERT: E 32 VAL cc_start: 0.8424 (t) cc_final: 0.8214 (m) REVERT: E 70 THR cc_start: 0.8160 (m) cc_final: 0.7959 (m) REVERT: E 83 VAL cc_start: 0.8477 (t) cc_final: 0.8246 (p) REVERT: E 129 LEU cc_start: 0.5886 (tt) cc_final: 0.5650 (tt) REVERT: E 205 TYR cc_start: 0.7105 (t80) cc_final: 0.6774 (t80) REVERT: E 220 LEU cc_start: 0.8143 (tt) cc_final: 0.7872 (tt) outliers start: 34 outliers final: 17 residues processed: 239 average time/residue: 0.6828 time to fit residues: 182.0173 Evaluate side-chains 238 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 32 VAL 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 248 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 113 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3629 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= 0.192 Angle : 0.517 8.467 12415 Z= 0.268 Chirality : 0.037 0.113 1410 Planarity : 0.004 0.056 1475 Dihedral : 5.357 53.608 1240 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.09 % Allowed : 19.89 % 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: 2.63 (0.24), residues: 1100 helix: 2.02 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.06 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 168 HIS 0.001 0.000 HIS A 76 PHE 0.016 0.001 PHE C 235 TYR 0.023 0.001 TYR D 111 ARG 0.009 0.001 ARG A 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 254 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7580 (tt) REVERT: A 147 MET cc_start: 0.6762 (ttt) cc_final: 0.6232 (ttt) REVERT: A 220 LEU cc_start: 0.8150 (tp) cc_final: 0.7831 (tm) REVERT: B 83 VAL cc_start: 0.8496 (t) cc_final: 0.8222 (p) REVERT: B 147 MET cc_start: 0.7111 (ttt) cc_final: 0.6549 (ttt) REVERT: B 220 LEU cc_start: 0.8149 (tt) cc_final: 0.7855 (tp) REVERT: C 147 MET cc_start: 0.7359 (ttt) cc_final: 0.7035 (ttt) REVERT: D 96 TYR cc_start: 0.8240 (m-80) cc_final: 0.7893 (m-80) REVERT: D 147 MET cc_start: 0.7201 (ttt) cc_final: 0.6812 (ttt) REVERT: D 163 MET cc_start: 0.6517 (tpp) cc_final: 0.6276 (tpp) REVERT: D 205 TYR cc_start: 0.6972 (t80) cc_final: 0.6742 (t80) REVERT: E 83 VAL cc_start: 0.8434 (t) cc_final: 0.8208 (p) REVERT: E 129 LEU cc_start: 0.5966 (tt) cc_final: 0.5741 (tt) REVERT: E 205 TYR cc_start: 0.7110 (t80) cc_final: 0.6807 (t80) REVERT: E 220 LEU cc_start: 0.8120 (tt) cc_final: 0.7825 (tt) outliers start: 28 outliers final: 19 residues processed: 239 average time/residue: 0.7031 time to fit residues: 187.0584 Evaluate side-chains 242 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL 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 74 PHE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 113 ILE 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 51 GLU Chi-restraints excluded: chain E residue 113 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9105 Z= 0.167 Angle : 0.533 10.277 12415 Z= 0.270 Chirality : 0.037 0.140 1410 Planarity : 0.004 0.055 1475 Dihedral : 5.225 51.712 1240 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.20 % Allowed : 19.89 % Favored : 76.91 % 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: 2.70 (0.24), residues: 1100 helix: 2.09 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.21 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 168 HIS 0.002 0.001 HIS A 76 PHE 0.017 0.001 PHE C 235 TYR 0.023 0.001 TYR D 111 ARG 0.008 0.001 ARG A 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 262 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7585 (tt) REVERT: A 147 MET cc_start: 0.6737 (ttt) cc_final: 0.6205 (ttt) REVERT: A 209 TYR cc_start: 0.6947 (m-80) cc_final: 0.6731 (m-80) REVERT: A 220 LEU cc_start: 0.8146 (tp) cc_final: 0.7875 (tm) REVERT: B 83 VAL cc_start: 0.8481 (t) cc_final: 0.8216 (p) REVERT: B 147 MET cc_start: 0.7099 (ttt) cc_final: 0.6565 (ttt) REVERT: B 220 LEU cc_start: 0.8146 (tt) cc_final: 0.7839 (tp) REVERT: C 147 MET cc_start: 0.7334 (ttt) cc_final: 0.6999 (ttt) REVERT: D 147 MET cc_start: 0.7150 (ttt) cc_final: 0.6752 (ttt) REVERT: D 163 MET cc_start: 0.6515 (tpp) cc_final: 0.6270 (tpp) REVERT: E 83 VAL cc_start: 0.8429 (t) cc_final: 0.8216 (p) REVERT: E 190 MET cc_start: 0.7958 (mtm) cc_final: 0.7706 (mtt) REVERT: E 205 TYR cc_start: 0.7112 (t80) cc_final: 0.6828 (t80) REVERT: E 220 LEU cc_start: 0.8116 (tt) cc_final: 0.7827 (tt) outliers start: 29 outliers final: 19 residues processed: 246 average time/residue: 0.6946 time to fit residues: 190.2203 Evaluate side-chains 246 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 74 PHE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 32 VAL 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 63 LEU 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 98 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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** E 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9105 Z= 0.168 Angle : 0.565 9.248 12415 Z= 0.282 Chirality : 0.037 0.183 1410 Planarity : 0.004 0.046 1475 Dihedral : 5.187 51.477 1240 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.65 % Allowed : 21.44 % Favored : 75.91 % 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: 2.73 (0.24), residues: 1100 helix: 2.12 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.23 (0.46), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 168 HIS 0.002 0.001 HIS E 76 PHE 0.017 0.001 PHE C 235 TYR 0.028 0.001 TYR D 96 ARG 0.006 0.001 ARG A 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 258 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7585 (tt) REVERT: A 147 MET cc_start: 0.6730 (ttt) cc_final: 0.6194 (ttt) REVERT: A 209 TYR cc_start: 0.6952 (m-80) cc_final: 0.6719 (m-80) REVERT: A 220 LEU cc_start: 0.8155 (tp) cc_final: 0.7882 (tm) REVERT: B 83 VAL cc_start: 0.8473 (t) cc_final: 0.8215 (p) REVERT: B 140 TYR cc_start: 0.7510 (t80) cc_final: 0.7272 (t80) REVERT: B 147 MET cc_start: 0.7090 (ttt) cc_final: 0.6598 (ttt) REVERT: B 189 THR cc_start: 0.8076 (t) cc_final: 0.7779 (p) REVERT: B 220 LEU cc_start: 0.8113 (tt) cc_final: 0.7806 (tp) REVERT: C 147 MET cc_start: 0.7331 (ttt) cc_final: 0.6983 (ttt) REVERT: D 147 MET cc_start: 0.7122 (ttt) cc_final: 0.6723 (ttt) REVERT: D 163 MET cc_start: 0.6519 (tpp) cc_final: 0.6250 (tpp) REVERT: E 83 VAL cc_start: 0.8391 (t) cc_final: 0.8186 (p) REVERT: E 205 TYR cc_start: 0.7111 (t80) cc_final: 0.6881 (t80) REVERT: E 220 LEU cc_start: 0.8116 (tt) cc_final: 0.7834 (tt) outliers start: 24 outliers final: 14 residues processed: 245 average time/residue: 0.7073 time to fit residues: 192.6257 Evaluate side-chains 242 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 227 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 B residue 74 PHE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 163 MET 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 C residue 248 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 63 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 49 optimal weight: 0.7980 chunk 72 optimal weight: 0.0470 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9105 Z= 0.169 Angle : 0.593 10.945 12415 Z= 0.295 Chirality : 0.038 0.217 1410 Planarity : 0.004 0.048 1475 Dihedral : 5.127 51.450 1240 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.99 % Allowed : 22.21 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.73 (0.25), residues: 1100 helix: 2.13 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.29 (0.46), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 168 HIS 0.002 0.001 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 A 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 251 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 233 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7648 (tt) REVERT: A 147 MET cc_start: 0.6738 (ttt) cc_final: 0.6239 (ttt) REVERT: A 220 LEU cc_start: 0.8142 (tp) cc_final: 0.7856 (tm) REVERT: B 83 VAL cc_start: 0.8451 (t) cc_final: 0.8208 (p) REVERT: B 147 MET cc_start: 0.7070 (ttt) cc_final: 0.6589 (ttt) REVERT: B 220 LEU cc_start: 0.8089 (tt) cc_final: 0.7786 (tp) REVERT: C 147 MET cc_start: 0.7321 (ttt) cc_final: 0.6970 (ttt) REVERT: D 96 TYR cc_start: 0.8200 (m-80) cc_final: 0.7849 (m-80) REVERT: D 147 MET cc_start: 0.7090 (ttt) cc_final: 0.6721 (ttt) REVERT: D 163 MET cc_start: 0.6502 (tpp) cc_final: 0.6235 (tpp) REVERT: E 70 THR cc_start: 0.8143 (m) cc_final: 0.7904 (m) REVERT: E 205 TYR cc_start: 0.7090 (t80) cc_final: 0.6831 (t80) REVERT: E 220 LEU cc_start: 0.8113 (tt) cc_final: 0.7816 (tt) outliers start: 18 outliers final: 13 residues processed: 243 average time/residue: 0.7035 time to fit residues: 190.0863 Evaluate side-chains 242 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 228 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 B residue 113 ILE Chi-restraints excluded: chain B residue 163 MET 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 C residue 248 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 63 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 80 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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** E 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.160841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.136946 restraints weight = 11630.724| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.00 r_work: 0.3690 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4127 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= 0.197 Angle : 0.622 13.295 12415 Z= 0.308 Chirality : 0.040 0.245 1410 Planarity : 0.004 0.047 1475 Dihedral : 5.154 50.631 1240 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.99 % Allowed : 22.65 % Favored : 75.36 % 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: 2.70 (0.24), residues: 1100 helix: 2.11 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.38 (0.45), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 168 HIS 0.003 0.001 HIS A 76 PHE 0.014 0.001 PHE C 235 TYR 0.023 0.001 TYR D 111 ARG 0.007 0.001 ARG A 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3322.25 seconds wall clock time: 60 minutes 17.93 seconds (3617.93 seconds total)