Starting phenix.real_space_refine on Thu Jul 2 04:59:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u15_26278/07_2026/7u15_26278.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u15_26278/07_2026/7u15_26278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u15_26278/07_2026/7u15_26278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u15_26278/07_2026/7u15_26278.map" model { file = "/net/cci-nas-00/data/ceres_data/7u15_26278/07_2026/7u15_26278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u15_26278/07_2026/7u15_26278.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7u15_26278/07_2026/7u15_26278.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u15_26278/07_2026/7u15_26278.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians S 21 5.16 5 C 2178 2.51 5 N 531 2.21 5 O 699 1.98 5 H 3255 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6684 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2172 Classifications: {'peptide': 135} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: A, C Time building chain proxies: 1.15, per 1000 atoms: 0.17 Number of scatterers: 6684 At special positions: 0 Unit cell: (93.183, 114.123, 39.786, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 O 699 8.00 N 531 7.00 C 2178 6.00 H 3255 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.03 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 Links applied NAG-ASN " NAG A 301 " - " ASN A 183 " " NAG A 302 " - " ASN A 145 " " NAG A 303 " - " ASN A 151 " " NAG A 304 " - " ASN A 164 " " NAG B 301 " - " ASN B 183 " " NAG B 302 " - " ASN B 145 " " NAG B 303 " - " ASN B 151 " " NAG B 304 " - " ASN B 164 " " NAG C 301 " - " ASN C 183 " " NAG C 302 " - " ASN C 145 " " NAG C 303 " - " ASN C 151 " " NAG C 304 " - " ASN C 164 " Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 232.7 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 123 removed outlier: 6.773A pdb=" N ASP B 122 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.649A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.475A pdb=" N VAL B 133 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 144 removed outlier: 6.827A pdb=" N TYR B 143 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.076A pdb=" N LEU B 150 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 156 through 158 removed outlier: 6.608A pdb=" N ASN B 156 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 171 removed outlier: 6.542A pdb=" N VAL B 169 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLN B 170 " --> pdb=" O PHE C 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 186 removed outlier: 6.623A pdb=" N THR B 185 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 191 removed outlier: 6.467A pdb=" N LEU B 190 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.381A pdb=" N ILE B 195 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 206 through 207 removed outlier: 7.009A pdb=" N GLU B 206 " --> pdb=" O MET A 207 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 210 through 212 removed outlier: 6.784A pdb=" N TYR B 211 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 217 through 219 removed outlier: 6.077A pdb=" N SER B 218 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 224 through 231 removed outlier: 6.833A pdb=" N THR A 231 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET C 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET B 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL C 230 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLN B 229 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 235 through 236 removed outlier: 6.851A pdb=" N THR B 235 " --> pdb=" O TYR A 236 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3255 1.03 - 1.23: 37 1.23 - 1.42: 1399 1.42 - 1.62: 2011 1.62 - 1.81: 36 Bond restraints: 6738 Sorted by residual: bond pdb=" C1 NAG B 302 " pdb=" O5 NAG B 302 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 8.94e+00 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C1 NAG C 302 " pdb=" O5 NAG C 302 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.78e+00 bond pdb=" CB ASP A 191 " pdb=" CG ASP A 191 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.18e+00 bond pdb=" CB ASP C 191 " pdb=" CG ASP C 191 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.16e+00 ... (remaining 6733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.38: 12030 5.38 - 10.76: 27 10.76 - 16.15: 3 16.15 - 21.53: 0 21.53 - 26.91: 9 Bond angle restraints: 12069 Sorted by residual: angle pdb=" CG2 THR A 235 " pdb=" CB THR A 235 " pdb=" HB THR A 235 " ideal model delta sigma weight residual 108.00 81.09 26.91 3.00e+00 1.11e-01 8.05e+01 angle pdb=" CG2 THR B 235 " pdb=" CB THR B 235 " pdb=" HB THR B 235 " ideal model delta sigma weight residual 108.00 81.14 26.86 3.00e+00 1.11e-01 8.02e+01 angle pdb=" CG2 THR C 235 " pdb=" CB THR C 235 " pdb=" HB THR C 235 " ideal model delta sigma weight residual 108.00 81.16 26.84 3.00e+00 1.11e-01 8.00e+01 angle pdb=" OG1 THR B 235 " pdb=" CB THR B 235 " pdb=" HB THR B 235 " ideal model delta sigma weight residual 109.00 82.96 26.04 3.00e+00 1.11e-01 7.53e+01 angle pdb=" OG1 THR C 235 " pdb=" CB THR C 235 " pdb=" HB THR C 235 " ideal model delta sigma weight residual 109.00 83.02 25.98 3.00e+00 1.11e-01 7.50e+01 ... (remaining 12064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 2599 16.15 - 32.31: 386 32.31 - 48.46: 66 48.46 - 64.61: 42 64.61 - 80.77: 15 Dihedral angle restraints: 3108 sinusoidal: 1677 harmonic: 1431 Sorted by residual: dihedral pdb=" CA ALA A 204 " pdb=" C ALA A 204 " pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ALA C 204 " pdb=" C ALA C 204 " pdb=" N GLU C 205 " pdb=" CA GLU C 205 " ideal model delta harmonic sigma weight residual 180.00 150.56 29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ALA B 204 " pdb=" C ALA B 204 " pdb=" N GLU B 205 " pdb=" CA GLU B 205 " ideal model delta harmonic sigma weight residual 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 3105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.293: 597 0.293 - 0.585: 3 0.585 - 0.878: 0 0.878 - 1.170: 0 1.170 - 1.463: 3 Chirality restraints: 603 Sorted by residual: chirality pdb=" CB THR A 235 " pdb=" CA THR A 235 " pdb=" OG1 THR A 235 " pdb=" CG2 THR A 235 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.35e+01 chirality pdb=" CB THR B 235 " pdb=" CA THR B 235 " pdb=" OG1 THR B 235 " pdb=" CG2 THR B 235 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.34e+01 chirality pdb=" CB THR C 235 " pdb=" CA THR C 235 " pdb=" OG1 THR C 235 " pdb=" CG2 THR C 235 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.34e+01 ... (remaining 600 not shown) Planarity restraints: 981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 145 " -0.037 2.00e-02 2.50e+03 2.83e-02 1.20e+01 pdb=" CG ASN A 145 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 145 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 145 " 0.028 2.00e-02 2.50e+03 pdb="HD21 ASN A 145 " 0.010 2.00e-02 2.50e+03 pdb=" C1 NAG A 302 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 145 " -0.037 2.00e-02 2.50e+03 2.82e-02 1.19e+01 pdb=" CG ASN C 145 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN C 145 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 145 " 0.028 2.00e-02 2.50e+03 pdb="HD21 ASN C 145 " 0.010 2.00e-02 2.50e+03 pdb=" C1 NAG C 302 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 145 " -0.037 2.00e-02 2.50e+03 2.81e-02 1.19e+01 pdb=" CG ASN B 145 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN B 145 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 145 " 0.028 2.00e-02 2.50e+03 pdb="HD21 ASN B 145 " 0.010 2.00e-02 2.50e+03 pdb=" C1 NAG B 302 " -0.037 2.00e-02 2.50e+03 ... (remaining 978 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 483 2.19 - 2.79: 13507 2.79 - 3.40: 17849 3.40 - 4.00: 24411 4.00 - 4.60: 34874 Nonbonded interactions: 91124 Sorted by model distance: nonbonded pdb=" H VAL B 128 " pdb=" O VAL C 128 " model vdw 1.591 2.450 nonbonded pdb=" O VAL B 128 " pdb=" H VAL A 128 " model vdw 1.612 2.450 nonbonded pdb=" OG SER B 240 " pdb=" HH TYR C 236 " model vdw 1.663 2.450 nonbonded pdb=" HH TYR B 236 " pdb=" OG SER A 240 " model vdw 1.680 2.450 nonbonded pdb=" O GLU B 205 " pdb=" H GLU C 206 " model vdw 1.745 2.450 ... (remaining 91119 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' } 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: 1.070 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: 0.040 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 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 : 0.006 0.060 3498 Z= 0.299 Angle : 1.293 17.194 4779 Z= 0.692 Chirality : 0.124 1.463 603 Planarity : 0.009 0.056 573 Dihedral : 17.785 69.314 1209 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.44 % Allowed : 33.86 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.51 (0.28), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.96 (0.21), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG B 180 TYR 0.028 0.003 TYR A 250 PHE 0.006 0.001 PHE B 237 HIS 0.011 0.004 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.30 ( 3483) covalent geometry : angle 1.21659 / 0.68 ( 4737) SS BOND : bond 0.00067 / 0.03 ( 3) SS BOND : angle 0.81106 / 0.43 ( 6) hydrogen bonds : bond 0.19149 / 13.07 ( 24) hydrogen bonds : angle 9.36521 / 6.36 ( 72) link_NAG-ASN : bond 0.00190 / 0.12 ( 12) link_NAG-ASN : angle 5.21103 / 3.42 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 ARG cc_start: 0.7214 (ptp90) cc_final: 0.6847 (ttp-110) REVERT: B 207 MET cc_start: 0.5623 (tmt) cc_final: 0.5315 (tmm) REVERT: A 124 LYS cc_start: 0.8111 (tppt) cc_final: 0.6241 (pptt) REVERT: A 180 ARG cc_start: 0.7229 (ptp90) cc_final: 0.6625 (mmm160) REVERT: A 207 MET cc_start: 0.5681 (tmt) cc_final: 0.5338 (tmm) REVERT: C 155 ASN cc_start: 0.7116 (m-40) cc_final: 0.6289 (p0) REVERT: C 180 ARG cc_start: 0.7527 (ptp90) cc_final: 0.6348 (ptp90) REVERT: C 207 MET cc_start: 0.6443 (tmt) cc_final: 0.6016 (tmm) REVERT: C 227 MET cc_start: 0.8210 (mtm) cc_final: 0.7970 (mtm) outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 0.5568 time to fit residues: 54.1944 Evaluate side-chains 78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN A 154 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN C 154 ASN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.224168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.205647 restraints weight = 12562.614| |-----------------------------------------------------------------------------| r_work (start): 0.4898 rms_B_bonded: 2.14 r_work: 0.4842 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4772 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.4772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3498 Z= 0.213 Angle : 0.827 11.538 4779 Z= 0.451 Chirality : 0.114 1.524 603 Planarity : 0.006 0.051 573 Dihedral : 7.633 40.849 467 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.05 % Favored : 80.95 % Rotamer: Outliers : 7.67 % Allowed : 27.25 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.20 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.72 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 180 TYR 0.025 0.002 TYR B 250 PHE 0.017 0.002 PHE B 213 HIS 0.010 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 ( 3483) covalent geometry : angle 0.81689 / 0.45 ( 4737) SS BOND : bond 0.00328 / 0.16 ( 3) SS BOND : angle 2.06662 / 1.13 ( 6) hydrogen bonds : bond 0.04779 / 3.31 ( 24) hydrogen bonds : angle 7.09177 / 5.02 ( 72) link_NAG-ASN : bond 0.00583 / 0.40 ( 12) link_NAG-ASN : angle 1.52703 / 1.01 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 178 LYS cc_start: 0.7132 (ptmm) cc_final: 0.5950 (pttt) REVERT: B 182 ASN cc_start: 0.7680 (t0) cc_final: 0.7451 (t0) REVERT: B 202 VAL cc_start: 0.6692 (OUTLIER) cc_final: 0.6405 (m) REVERT: B 207 MET cc_start: 0.5947 (tmt) cc_final: 0.5414 (tmm) REVERT: B 241 GLU cc_start: 0.8144 (tt0) cc_final: 0.7911 (tt0) REVERT: A 124 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.6105 (pptt) REVERT: A 180 ARG cc_start: 0.7556 (ptp90) cc_final: 0.6628 (mmp-170) REVERT: A 207 MET cc_start: 0.5898 (tmt) cc_final: 0.5377 (tmm) REVERT: A 239 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.7634 (p-80) REVERT: A 247 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.5974 (mtp85) REVERT: C 124 LYS cc_start: 0.8449 (mptm) cc_final: 0.8218 (tppp) REVERT: C 150 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7700 (mt) REVERT: C 178 LYS cc_start: 0.7213 (ptmm) cc_final: 0.6835 (mtmm) REVERT: C 180 ARG cc_start: 0.7930 (ptp90) cc_final: 0.6443 (ptt90) REVERT: C 207 MET cc_start: 0.6597 (tmt) cc_final: 0.6085 (tmm) outliers start: 29 outliers final: 7 residues processed: 112 average time/residue: 0.5658 time to fit residues: 66.0430 Evaluate side-chains 99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 0.0060 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.221624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.203446 restraints weight = 12323.690| |-----------------------------------------------------------------------------| r_work (start): 0.4887 rms_B_bonded: 2.05 r_work: 0.4836 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4771 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3498 Z= 0.153 Angle : 0.723 11.494 4779 Z= 0.404 Chirality : 0.113 1.452 603 Planarity : 0.004 0.048 573 Dihedral : 6.343 23.006 451 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 6.08 % Allowed : 28.04 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.83 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.44 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 180 TYR 0.014 0.001 TYR C 143 PHE 0.006 0.001 PHE C 171 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 3483) covalent geometry : angle 0.71374 / 0.40 ( 4737) SS BOND : bond 0.00219 / 0.11 ( 3) SS BOND : angle 0.87764 / 0.50 ( 6) hydrogen bonds : bond 0.04513 / 3.18 ( 24) hydrogen bonds : angle 6.32405 / 4.47 ( 72) link_NAG-ASN : bond 0.00255 / 0.18 ( 12) link_NAG-ASN : angle 1.51296 / 0.95 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: B 178 LYS cc_start: 0.7100 (ptmm) cc_final: 0.6118 (pttt) REVERT: B 207 MET cc_start: 0.5911 (tmt) cc_final: 0.5480 (tmm) REVERT: B 241 GLU cc_start: 0.8098 (tt0) cc_final: 0.7851 (tt0) REVERT: A 124 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.6067 (pptt) REVERT: A 168 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: A 180 ARG cc_start: 0.7491 (ptp90) cc_final: 0.6377 (mmm160) REVERT: A 207 MET cc_start: 0.6127 (tmt) cc_final: 0.5608 (tmm) REVERT: A 247 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.5898 (mtp85) REVERT: C 150 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7983 (mt) REVERT: C 163 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: C 178 LYS cc_start: 0.6999 (ptmm) cc_final: 0.6733 (mtmm) REVERT: C 180 ARG cc_start: 0.7993 (ptp90) cc_final: 0.6750 (ptt90) REVERT: C 207 MET cc_start: 0.6635 (tmt) cc_final: 0.6125 (tmm) REVERT: C 215 THR cc_start: 0.8237 (p) cc_final: 0.7802 (t) REVERT: C 250 TYR cc_start: 0.7604 (p90) cc_final: 0.5114 (t80) outliers start: 23 outliers final: 9 residues processed: 103 average time/residue: 0.5520 time to fit residues: 59.3692 Evaluate side-chains 92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN ** A 155 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 = 0.4886 r_free = 0.4886 target = 0.206646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.187057 restraints weight = 12424.816| |-----------------------------------------------------------------------------| r_work (start): 0.4731 rms_B_bonded: 2.13 r_work: 0.4678 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4606 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3498 Z= 0.200 Angle : 0.766 11.522 4779 Z= 0.422 Chirality : 0.113 1.464 603 Planarity : 0.005 0.054 573 Dihedral : 6.080 19.517 451 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.30 % Favored : 79.70 % Rotamer: Outliers : 8.20 % Allowed : 26.72 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.60 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.26 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 180 TYR 0.018 0.002 TYR C 143 PHE 0.007 0.002 PHE B 171 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 ( 3483) covalent geometry : angle 0.74967 / 0.42 ( 4737) SS BOND : bond 0.00375 / 0.18 ( 3) SS BOND : angle 1.72303 / 0.93 ( 6) hydrogen bonds : bond 0.03573 / 2.52 ( 24) hydrogen bonds : angle 6.01754 / 4.31 ( 72) link_NAG-ASN : bond 0.00292 / 0.20 ( 12) link_NAG-ASN : angle 1.83831 / 1.31 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.6348 (tmt) cc_final: 0.5889 (tmm) REVERT: B 241 GLU cc_start: 0.8058 (tt0) cc_final: 0.7824 (tt0) REVERT: A 124 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.6083 (pptt) REVERT: A 207 MET cc_start: 0.6371 (OUTLIER) cc_final: 0.5883 (tmm) REVERT: C 124 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8377 (tppp) REVERT: C 163 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: C 165 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7566 (pt) REVERT: C 168 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: C 178 LYS cc_start: 0.7651 (ptmm) cc_final: 0.7319 (ptmt) REVERT: C 207 MET cc_start: 0.6936 (tmt) cc_final: 0.6341 (tmm) outliers start: 31 outliers final: 14 residues processed: 114 average time/residue: 0.4415 time to fit residues: 53.0194 Evaluate side-chains 107 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 221 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 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 = 0.4933 r_free = 0.4933 target = 0.210371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.191329 restraints weight = 12486.774| |-----------------------------------------------------------------------------| r_work (start): 0.4787 rms_B_bonded: 2.15 r_work: 0.4733 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4663 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3498 Z= 0.146 Angle : 0.699 11.374 4779 Z= 0.390 Chirality : 0.111 1.422 603 Planarity : 0.004 0.047 573 Dihedral : 5.925 18.665 451 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.05 % Favored : 81.95 % Rotamer: Outliers : 6.88 % Allowed : 31.22 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.49 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.18 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 180 TYR 0.019 0.001 TYR B 143 PHE 0.011 0.002 PHE B 213 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 3483) covalent geometry : angle 0.68760 / 0.39 ( 4737) SS BOND : bond 0.00074 / 0.04 ( 3) SS BOND : angle 0.81445 / 0.45 ( 6) hydrogen bonds : bond 0.03750 / 2.68 ( 24) hydrogen bonds : angle 5.75036 / 4.17 ( 72) link_NAG-ASN : bond 0.00166 / 0.11 ( 12) link_NAG-ASN : angle 1.58860 / 1.01 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.6611 (tmt) cc_final: 0.6098 (tmm) REVERT: B 239 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7360 (p-80) REVERT: B 241 GLU cc_start: 0.8032 (tt0) cc_final: 0.7712 (tt0) REVERT: A 124 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.5979 (pptt) REVERT: A 180 ARG cc_start: 0.7462 (ptp90) cc_final: 0.7212 (pmm-80) REVERT: A 207 MET cc_start: 0.6405 (tmt) cc_final: 0.5876 (tmm) REVERT: A 247 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.6054 (mtp85) REVERT: C 163 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: C 178 LYS cc_start: 0.7717 (ptmm) cc_final: 0.6896 (pttt) REVERT: C 192 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6664 (mtt) REVERT: C 207 MET cc_start: 0.6959 (tmt) cc_final: 0.6469 (tmm) REVERT: C 215 THR cc_start: 0.8056 (p) cc_final: 0.7400 (t) REVERT: C 250 TYR cc_start: 0.8342 (p90) cc_final: 0.4806 (t80) outliers start: 26 outliers final: 12 residues processed: 107 average time/residue: 0.4944 time to fit residues: 55.6349 Evaluate side-chains 99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 GLN A 155 ASN A 242 GLN C 156 ASN C 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.204795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.186055 restraints weight = 12463.515| |-----------------------------------------------------------------------------| r_work (start): 0.4751 rms_B_bonded: 2.09 r_work: 0.4695 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4625 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.4625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3498 Z= 0.154 Angle : 0.687 11.437 4779 Z= 0.382 Chirality : 0.111 1.426 603 Planarity : 0.004 0.046 573 Dihedral : 5.704 18.408 451 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.55 % Favored : 80.45 % Rotamer: Outliers : 8.47 % Allowed : 29.37 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.45 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.15 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 180 TYR 0.020 0.002 TYR B 143 PHE 0.006 0.001 PHE C 171 HIS 0.005 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 3483) covalent geometry : angle 0.67639 / 0.38 ( 4737) SS BOND : bond 0.00121 / 0.06 ( 3) SS BOND : angle 0.90889 / 0.50 ( 6) hydrogen bonds : bond 0.03452 / 2.48 ( 24) hydrogen bonds : angle 5.57804 / 4.08 ( 72) link_NAG-ASN : bond 0.00180 / 0.12 ( 12) link_NAG-ASN : angle 1.49888 / 0.95 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: B 180 ARG cc_start: 0.7515 (ptp90) cc_final: 0.7064 (pmm-80) REVERT: B 207 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6289 (tmm) REVERT: B 239 HIS cc_start: 0.7983 (OUTLIER) cc_final: 0.7264 (p-80) REVERT: B 241 GLU cc_start: 0.8029 (tt0) cc_final: 0.7742 (tt0) REVERT: A 124 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.5734 (pptt) REVERT: A 205 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.5968 (mm-30) REVERT: A 207 MET cc_start: 0.6508 (OUTLIER) cc_final: 0.5900 (tmm) REVERT: A 239 HIS cc_start: 0.7689 (OUTLIER) cc_final: 0.7374 (p-80) REVERT: A 247 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.5974 (mtp85) REVERT: C 150 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8547 (mt) REVERT: C 161 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6870 (mt-10) REVERT: C 163 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: C 178 LYS cc_start: 0.7816 (ptmm) cc_final: 0.7421 (ptmt) REVERT: C 192 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6731 (mtt) REVERT: C 207 MET cc_start: 0.7047 (tmt) cc_final: 0.6502 (tmm) REVERT: C 215 THR cc_start: 0.8096 (p) cc_final: 0.7398 (t) REVERT: C 239 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.6811 (p-80) outliers start: 32 outliers final: 15 residues processed: 110 average time/residue: 0.4848 time to fit residues: 55.9610 Evaluate side-chains 116 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 239 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN A 242 GLN C 148 ASN C 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.210266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.192022 restraints weight = 12212.641| |-----------------------------------------------------------------------------| r_work (start): 0.4809 rms_B_bonded: 2.09 r_work: 0.4754 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4684 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.7116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3498 Z= 0.109 Angle : 0.651 11.333 4779 Z= 0.364 Chirality : 0.110 1.409 603 Planarity : 0.004 0.043 573 Dihedral : 5.648 17.743 451 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer: Outliers : 5.82 % Allowed : 31.48 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.40 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 180 TYR 0.015 0.001 TYR C 143 PHE 0.006 0.001 PHE C 237 HIS 0.001 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 3483) covalent geometry : angle 0.64237 / 0.36 ( 4737) SS BOND : bond 0.00088 / 0.04 ( 3) SS BOND : angle 0.40555 / 0.22 ( 6) hydrogen bonds : bond 0.03617 / 2.58 ( 24) hydrogen bonds : angle 5.47922 / 4.03 ( 72) link_NAG-ASN : bond 0.00167 / 0.12 ( 12) link_NAG-ASN : angle 1.39997 / 0.87 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: B 180 ARG cc_start: 0.7473 (ptp90) cc_final: 0.7149 (pmm-80) REVERT: B 182 ASN cc_start: 0.8539 (t0) cc_final: 0.8235 (t0) REVERT: B 207 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.6217 (tmm) REVERT: B 241 GLU cc_start: 0.8022 (tt0) cc_final: 0.7713 (tt0) REVERT: A 207 MET cc_start: 0.6473 (tmt) cc_final: 0.5873 (tmm) REVERT: A 239 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.7303 (p-80) REVERT: A 247 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.5904 (mtp85) REVERT: C 161 GLU cc_start: 0.7597 (mt-10) cc_final: 0.6930 (mt-10) REVERT: C 168 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: C 178 LYS cc_start: 0.7797 (ptmm) cc_final: 0.7045 (pttt) REVERT: C 192 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6393 (mtt) REVERT: C 207 MET cc_start: 0.7039 (tmt) cc_final: 0.6481 (tmm) REVERT: C 215 THR cc_start: 0.7469 (p) cc_final: 0.6827 (t) outliers start: 22 outliers final: 10 residues processed: 101 average time/residue: 0.4841 time to fit residues: 51.1750 Evaluate side-chains 98 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN A 242 GLN C 148 ASN C 156 ASN C 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.193392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.173748 restraints weight = 12442.832| |-----------------------------------------------------------------------------| r_work (start): 0.4622 rms_B_bonded: 2.17 r_work: 0.4565 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4494 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.7691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3498 Z= 0.248 Angle : 0.779 11.593 4779 Z= 0.431 Chirality : 0.114 1.468 603 Planarity : 0.005 0.048 573 Dihedral : 6.023 20.846 451 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.55 % Favored : 79.45 % Rotamer: Outliers : 6.88 % Allowed : 29.37 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.44 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 247 TYR 0.025 0.002 TYR C 143 PHE 0.008 0.001 PHE A 171 HIS 0.004 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 ( 3483) covalent geometry : angle 0.76190 / 0.43 ( 4737) SS BOND : bond 0.00192 / 0.09 ( 3) SS BOND : angle 1.54629 / 0.81 ( 6) hydrogen bonds : bond 0.03530 / 2.46 ( 24) hydrogen bonds : angle 5.77905 / 4.25 ( 72) link_NAG-ASN : bond 0.00183 / 0.12 ( 12) link_NAG-ASN : angle 1.95120 / 1.28 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 148 ASN cc_start: 0.8432 (m110) cc_final: 0.8211 (m-40) REVERT: B 161 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7601 (mt-10) REVERT: B 182 ASN cc_start: 0.8563 (t0) cc_final: 0.8240 (t0) REVERT: B 207 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6320 (tmm) REVERT: B 239 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7532 (p-80) REVERT: B 241 GLU cc_start: 0.8089 (tt0) cc_final: 0.7780 (tt0) REVERT: A 207 MET cc_start: 0.6735 (OUTLIER) cc_final: 0.6166 (tmm) REVERT: C 168 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: C 178 LYS cc_start: 0.7881 (ptmm) cc_final: 0.7556 (ptmt) REVERT: C 207 MET cc_start: 0.7160 (tmt) cc_final: 0.6583 (tmm) REVERT: C 212 ASP cc_start: 0.7950 (m-30) cc_final: 0.7714 (m-30) REVERT: C 239 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.7436 (p-80) outliers start: 26 outliers final: 15 residues processed: 100 average time/residue: 0.4371 time to fit residues: 46.1244 Evaluate side-chains 102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN A 242 GLN C 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.198965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.180169 restraints weight = 12396.954| |-----------------------------------------------------------------------------| r_work (start): 0.4688 rms_B_bonded: 2.18 r_work: 0.4634 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4563 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.7925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3498 Z= 0.163 Angle : 0.696 11.503 4779 Z= 0.389 Chirality : 0.112 1.439 603 Planarity : 0.004 0.047 573 Dihedral : 5.886 19.978 451 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.80 % Favored : 81.20 % Rotamer: Outliers : 5.56 % Allowed : 32.28 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.47 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 180 TYR 0.020 0.002 TYR C 143 PHE 0.009 0.001 PHE C 171 HIS 0.002 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 3483) covalent geometry : angle 0.68321 / 0.39 ( 4737) SS BOND : bond 0.00103 / 0.05 ( 3) SS BOND : angle 0.82360 / 0.44 ( 6) hydrogen bonds : bond 0.03660 / 2.60 ( 24) hydrogen bonds : angle 5.78804 / 4.29 ( 72) link_NAG-ASN : bond 0.00108 / 0.07 ( 12) link_NAG-ASN : angle 1.65334 / 1.06 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7741 (mt-10) REVERT: B 207 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6433 (tmm) REVERT: B 241 GLU cc_start: 0.8083 (tt0) cc_final: 0.7779 (tt0) REVERT: A 163 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: A 207 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6213 (tmm) REVERT: C 163 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: C 168 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: C 178 LYS cc_start: 0.7929 (ptmm) cc_final: 0.7257 (pttt) REVERT: C 192 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.6891 (mtt) REVERT: C 207 MET cc_start: 0.7134 (tmt) cc_final: 0.6544 (tmm) REVERT: C 212 ASP cc_start: 0.8007 (m-30) cc_final: 0.7756 (m-30) REVERT: C 239 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.7070 (p-80) outliers start: 21 outliers final: 13 residues processed: 96 average time/residue: 0.4495 time to fit residues: 45.5350 Evaluate side-chains 99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 0.2980 chunk 21 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.199548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.181055 restraints weight = 12246.409| |-----------------------------------------------------------------------------| r_work (start): 0.4711 rms_B_bonded: 2.13 r_work: 0.4655 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4582 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.4582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.8059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3498 Z= 0.161 Angle : 0.686 11.538 4779 Z= 0.384 Chirality : 0.112 1.450 603 Planarity : 0.004 0.044 573 Dihedral : 5.808 19.611 451 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.80 % Favored : 81.20 % Rotamer: Outliers : 5.29 % Allowed : 32.54 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.46 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.15 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 180 TYR 0.018 0.002 TYR C 143 PHE 0.005 0.001 PHE C 237 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 3483) covalent geometry : angle 0.67343 / 0.38 ( 4737) SS BOND : bond 0.00135 / 0.07 ( 3) SS BOND : angle 0.78312 / 0.41 ( 6) hydrogen bonds : bond 0.03557 / 2.54 ( 24) hydrogen bonds : angle 5.79477 / 4.30 ( 72) link_NAG-ASN : bond 0.00108 / 0.08 ( 12) link_NAG-ASN : angle 1.61750 / 1.04 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7701 (mt-10) REVERT: B 207 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6411 (tmm) REVERT: B 241 GLU cc_start: 0.8073 (tt0) cc_final: 0.7757 (tt0) REVERT: A 163 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: A 207 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6213 (tmm) REVERT: A 236 TYR cc_start: 0.9162 (t80) cc_final: 0.8917 (t80) REVERT: A 239 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7296 (p-80) REVERT: C 168 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: C 178 LYS cc_start: 0.7891 (ptmm) cc_final: 0.7213 (pttt) REVERT: C 192 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6868 (mtt) REVERT: C 207 MET cc_start: 0.7183 (tmt) cc_final: 0.6589 (tmm) REVERT: C 212 ASP cc_start: 0.8024 (m-30) cc_final: 0.7756 (m-30) REVERT: C 239 HIS cc_start: 0.7555 (OUTLIER) cc_final: 0.6902 (p-80) outliers start: 20 outliers final: 12 residues processed: 92 average time/residue: 0.4446 time to fit residues: 43.3231 Evaluate side-chains 96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 148 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 = 0.4824 r_free = 0.4824 target = 0.198651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.180084 restraints weight = 12252.469| |-----------------------------------------------------------------------------| r_work (start): 0.4694 rms_B_bonded: 2.16 r_work: 0.4636 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4565 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.4565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.8195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3498 Z= 0.180 Angle : 0.704 11.592 4779 Z= 0.394 Chirality : 0.113 1.466 603 Planarity : 0.004 0.045 573 Dihedral : 5.884 19.354 451 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.05 % Favored : 79.95 % Rotamer: Outliers : 5.82 % Allowed : 32.80 % Favored : 61.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.47 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.17 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 180 TYR 0.018 0.002 TYR C 143 PHE 0.005 0.001 PHE C 237 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 3483) covalent geometry : angle 0.69021 / 0.39 ( 4737) SS BOND : bond 0.00118 / 0.06 ( 3) SS BOND : angle 0.91427 / 0.48 ( 6) hydrogen bonds : bond 0.03696 / 2.61 ( 24) hydrogen bonds : angle 5.79390 / 4.28 ( 72) link_NAG-ASN : bond 0.00124 / 0.09 ( 12) link_NAG-ASN : angle 1.69595 / 1.10 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2270.08 seconds wall clock time: 39 minutes 4.33 seconds (2344.33 seconds total)