Starting phenix.real_space_refine on Tue Mar 3 15:54:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u15_26278/03_2026/7u15_26278.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u15_26278/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7u15_26278/03_2026/7u15_26278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u15_26278/03_2026/7u15_26278.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u15_26278/03_2026/7u15_26278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u15_26278/03_2026/7u15_26278.map" } 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-5986/lib/python3.9/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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: A, C Time building chain proxies: 1.08, per 1000 atoms: 0.16 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: 0.64 Conformation dependent library (CDL) restraints added in 340.1 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: 0.18 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: 1.27 Time building geometry restraints manager: 0.86 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: 2815 16.15 - 32.31: 410 32.31 - 48.46: 66 48.46 - 64.61: 54 64.61 - 80.77: 15 Dihedral angle restraints: 3360 sinusoidal: 1929 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 3357 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: 1.840 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.510 Find NCS groups from input model: 0.040 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:9.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 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 : 17.227 69.314 1461 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 covalent geometry : bond 0.00630 ( 3483) covalent geometry : angle 1.21659 ( 4737) SS BOND : bond 0.00067 ( 3) SS BOND : angle 0.81106 ( 6) hydrogen bonds : bond 0.19149 ( 24) hydrogen bonds : angle 9.36521 ( 72) link_NAG-ASN : bond 0.00190 ( 12) link_NAG-ASN : angle 5.21103 ( 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 : 0.177 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: 0.6896 time to fit residues: 67.0298 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 : 0.227 ------------------------------------------------------------------------------- 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.222785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.204360 restraints weight = 12579.792| |-----------------------------------------------------------------------------| r_work (start): 0.4880 rms_B_bonded: 2.12 r_work: 0.4827 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4760 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3498 Z= 0.217 Angle : 0.826 11.618 4779 Z= 0.454 Chirality : 0.115 1.530 603 Planarity : 0.006 0.050 573 Dihedral : 7.932 41.705 719 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 19.05 % Favored : 80.70 % Rotamer: Outliers : 7.67 % Allowed : 27.78 % Favored : 64.55 % 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 0.004 0.001 ARG A 180 TYR 0.023 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 covalent geometry : bond 0.00481 ( 3483) covalent geometry : angle 0.81649 ( 4737) SS BOND : bond 0.00184 ( 3) SS BOND : angle 2.24328 ( 6) hydrogen bonds : bond 0.04748 ( 24) hydrogen bonds : angle 7.05352 ( 72) link_NAG-ASN : bond 0.00787 ( 12) link_NAG-ASN : angle 1.43028 ( 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 127 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 168 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: B 182 ASN cc_start: 0.7692 (t0) cc_final: 0.7480 (t0) REVERT: B 202 VAL cc_start: 0.6801 (OUTLIER) cc_final: 0.6521 (m) REVERT: B 207 MET cc_start: 0.5972 (tmt) cc_final: 0.5486 (tmm) REVERT: B 241 GLU cc_start: 0.8098 (tt0) cc_final: 0.7867 (tt0) REVERT: B 246 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7349 (mt-10) REVERT: A 124 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.6193 (pptt) REVERT: A 168 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: A 180 ARG cc_start: 0.7609 (ptp90) cc_final: 0.6693 (mmm160) REVERT: A 207 MET cc_start: 0.5939 (tmt) cc_final: 0.5438 (tmm) REVERT: A 239 HIS cc_start: 0.8044 (OUTLIER) cc_final: 0.7747 (p-80) REVERT: A 247 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.6051 (mtp85) REVERT: C 124 LYS cc_start: 0.8604 (mptm) cc_final: 0.8375 (tppp) REVERT: C 150 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7745 (mt) REVERT: C 178 LYS cc_start: 0.7318 (ptmm) cc_final: 0.6778 (mtmt) REVERT: C 180 ARG cc_start: 0.7932 (ptp90) cc_final: 0.6495 (ptt90) REVERT: C 207 MET cc_start: 0.6600 (tmt) cc_final: 0.6110 (tmm) REVERT: C 241 GLU cc_start: 0.8211 (tt0) cc_final: 0.7898 (tt0) outliers start: 29 outliers final: 8 residues processed: 117 average time/residue: 0.7799 time to fit residues: 94.8207 Evaluate side-chains 95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 168 GLN 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 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 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: 0.6980 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 0.0070 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** 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 = 0.5092 r_free = 0.5092 target = 0.230804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.212861 restraints weight = 12473.069| |-----------------------------------------------------------------------------| r_work (start): 0.4983 rms_B_bonded: 2.12 r_work: 0.4933 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4867 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.4867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3498 Z= 0.119 Angle : 0.696 11.372 4779 Z= 0.387 Chirality : 0.110 1.420 603 Planarity : 0.004 0.043 573 Dihedral : 6.557 35.859 704 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.79 % Favored : 85.21 % Rotamer: Outliers : 4.76 % Allowed : 31.22 % Favored : 64.02 % 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: -5.92 (0.29), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.50 (0.22), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 180 TYR 0.014 0.001 TYR C 250 PHE 0.005 0.001 PHE C 237 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3483) covalent geometry : angle 0.68535 ( 4737) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.46391 ( 6) hydrogen bonds : bond 0.04335 ( 24) hydrogen bonds : angle 6.21154 ( 72) link_NAG-ASN : bond 0.00260 ( 12) link_NAG-ASN : angle 1.54158 ( 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 96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.178 Fit side-chains REVERT: B 182 ASN cc_start: 0.7495 (t0) cc_final: 0.7288 (t0) REVERT: B 241 GLU cc_start: 0.8025 (tt0) cc_final: 0.7773 (tt0) REVERT: A 124 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.5834 (pptt) REVERT: A 163 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: A 180 ARG cc_start: 0.7398 (ptp90) cc_final: 0.6250 (mmm160) REVERT: A 207 MET cc_start: 0.5965 (tmt) cc_final: 0.5516 (tmt) REVERT: A 239 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.7624 (p-80) REVERT: A 247 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.5877 (mtp85) REVERT: C 150 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7769 (mt) REVERT: C 180 ARG cc_start: 0.8021 (ptp90) cc_final: 0.6809 (ptt90) REVERT: C 207 MET cc_start: 0.6498 (tmt) cc_final: 0.5937 (tmm) REVERT: C 215 THR cc_start: 0.7965 (p) cc_final: 0.7602 (t) REVERT: C 227 MET cc_start: 0.8941 (mtm) cc_final: 0.8548 (mtm) REVERT: C 250 TYR cc_start: 0.7419 (p90) cc_final: 0.5069 (t80) outliers start: 18 outliers final: 6 residues processed: 91 average time/residue: 0.7636 time to fit residues: 72.3077 Evaluate side-chains 82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 163 GLU 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 150 LEU 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: 8.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** 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 = 0.4977 r_free = 0.4977 target = 0.217715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.198835 restraints weight = 12465.098| |-----------------------------------------------------------------------------| r_work (start): 0.4838 rms_B_bonded: 2.05 r_work: 0.4781 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4711 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3498 Z= 0.156 Angle : 0.710 11.513 4779 Z= 0.391 Chirality : 0.112 1.441 603 Planarity : 0.004 0.042 573 Dihedral : 6.208 32.691 703 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.05 % Favored : 80.95 % Rotamer: Outliers : 6.08 % Allowed : 29.10 % Favored : 64.81 % 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: -5.65 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 180 TYR 0.015 0.002 TYR C 143 PHE 0.006 0.001 PHE C 171 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3483) covalent geometry : angle 0.69719 ( 4737) SS BOND : bond 0.00270 ( 3) SS BOND : angle 1.27249 ( 6) hydrogen bonds : bond 0.03375 ( 24) hydrogen bonds : angle 5.82141 ( 72) link_NAG-ASN : bond 0.00310 ( 12) link_NAG-ASN : angle 1.61242 ( 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 118 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: B 207 MET cc_start: 0.5791 (tpt) cc_final: 0.5194 (tmm) REVERT: B 241 GLU cc_start: 0.8002 (tt0) cc_final: 0.7791 (tt0) REVERT: A 124 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.6172 (pptt) REVERT: A 163 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: A 180 ARG cc_start: 0.7575 (ptp90) cc_final: 0.6444 (mmm160) REVERT: A 207 MET cc_start: 0.5955 (OUTLIER) cc_final: 0.5563 (tmm) REVERT: A 247 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.6087 (mtp85) REVERT: C 150 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7880 (mt) REVERT: C 163 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: C 178 LYS cc_start: 0.7396 (ptmm) cc_final: 0.6685 (mtmt) REVERT: C 180 ARG cc_start: 0.8014 (ptp90) cc_final: 0.6690 (ptt90) REVERT: C 207 MET cc_start: 0.6851 (tmt) cc_final: 0.6288 (tmm) REVERT: C 215 THR cc_start: 0.7608 (p) cc_final: 0.7307 (t) REVERT: C 250 TYR cc_start: 0.7756 (p90) cc_final: 0.5046 (t80) outliers start: 23 outliers final: 12 residues processed: 109 average time/residue: 0.6729 time to fit residues: 76.7596 Evaluate side-chains 103 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 170 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 THR 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 163 GLU 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 150 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 0.0370 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** 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 = 0.5001 r_free = 0.5001 target = 0.219034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.200821 restraints weight = 12520.481| |-----------------------------------------------------------------------------| r_work (start): 0.4876 rms_B_bonded: 2.06 r_work: 0.4823 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4752 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.4752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3498 Z= 0.117 Angle : 0.657 11.352 4779 Z= 0.366 Chirality : 0.110 1.415 603 Planarity : 0.003 0.039 573 Dihedral : 5.990 34.369 703 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 4.76 % Allowed : 31.22 % Favored : 64.02 % 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: -5.50 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 180 TYR 0.012 0.001 TYR C 143 PHE 0.005 0.001 PHE C 171 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3483) covalent geometry : angle 0.64588 ( 4737) SS BOND : bond 0.00102 ( 3) SS BOND : angle 0.50547 ( 6) hydrogen bonds : bond 0.03534 ( 24) hydrogen bonds : angle 5.62853 ( 72) link_NAG-ASN : bond 0.00202 ( 12) link_NAG-ASN : angle 1.54896 ( 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 107 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.5917 (tpt) cc_final: 0.5470 (tmm) REVERT: B 241 GLU cc_start: 0.7975 (tt0) cc_final: 0.7688 (tt0) REVERT: A 180 ARG cc_start: 0.7558 (ptp90) cc_final: 0.6466 (mmm160) REVERT: A 207 MET cc_start: 0.5949 (tmt) cc_final: 0.5596 (tmm) REVERT: A 247 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.5969 (mtp85) REVERT: C 150 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7967 (mt) REVERT: C 163 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: C 178 LYS cc_start: 0.7388 (ptmm) cc_final: 0.6624 (pttt) REVERT: C 180 ARG cc_start: 0.8029 (ptp90) cc_final: 0.6747 (ptt90) REVERT: C 207 MET cc_start: 0.6810 (tmt) cc_final: 0.6201 (tmm) REVERT: C 215 THR cc_start: 0.7400 (p) cc_final: 0.7029 (t) REVERT: C 250 TYR cc_start: 0.7856 (p90) cc_final: 0.4927 (t80) outliers start: 18 outliers final: 9 residues processed: 101 average time/residue: 0.6279 time to fit residues: 66.3584 Evaluate side-chains 96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL 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 150 LEU 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: 2.9990 chunk 8 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.0670 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4936 r_free = 0.4936 target = 0.211145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.192396 restraints weight = 12492.624| |-----------------------------------------------------------------------------| r_work (start): 0.4807 rms_B_bonded: 2.08 r_work: 0.4750 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4678 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.4678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3498 Z= 0.146 Angle : 0.678 11.451 4779 Z= 0.376 Chirality : 0.111 1.429 603 Planarity : 0.004 0.039 573 Dihedral : 5.900 33.627 702 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.80 % Favored : 81.20 % Rotamer: Outliers : 6.88 % Allowed : 30.16 % Favored : 62.96 % 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 0.007 0.001 ARG B 180 TYR 0.015 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 covalent geometry : bond 0.00337 ( 3483) covalent geometry : angle 0.66506 ( 4737) SS BOND : bond 0.00153 ( 3) SS BOND : angle 0.98589 ( 6) hydrogen bonds : bond 0.03236 ( 24) hydrogen bonds : angle 5.41603 ( 72) link_NAG-ASN : bond 0.00222 ( 12) link_NAG-ASN : angle 1.64140 ( 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 118 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: B 207 MET cc_start: 0.5909 (tpt) cc_final: 0.5624 (tmm) REVERT: B 239 HIS cc_start: 0.8038 (OUTLIER) cc_final: 0.7369 (p-80) REVERT: B 241 GLU cc_start: 0.7989 (tt0) cc_final: 0.7693 (tt0) REVERT: A 132 TYR cc_start: 0.8661 (t80) cc_final: 0.8320 (t80) REVERT: A 168 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: A 207 MET cc_start: 0.6045 (OUTLIER) cc_final: 0.5750 (tmm) REVERT: A 239 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.7422 (p-80) REVERT: A 247 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.5983 (mtp85) REVERT: C 132 TYR cc_start: 0.7877 (t80) cc_final: 0.7591 (t80) REVERT: C 150 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8277 (mt) REVERT: C 163 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: C 178 LYS cc_start: 0.7625 (ptmm) cc_final: 0.6776 (pttt) REVERT: C 207 MET cc_start: 0.6975 (tmt) cc_final: 0.6423 (tmm) REVERT: C 215 THR cc_start: 0.7649 (p) cc_final: 0.7198 (t) REVERT: C 250 TYR cc_start: 0.8109 (p90) cc_final: 0.4867 (t80) outliers start: 26 outliers final: 16 residues processed: 110 average time/residue: 0.6113 time to fit residues: 70.6452 Evaluate side-chains 111 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 163 GLU Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 SER 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 208 SER 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 150 LEU Chi-restraints excluded: chain C residue 163 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN B 242 GLN A 154 ASN A 155 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN C 148 ASN C 154 ASN C 156 ASN C 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.215534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.196727 restraints weight = 12122.499| |-----------------------------------------------------------------------------| r_work (start): 0.4879 rms_B_bonded: 2.08 r_work: 0.4825 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4754 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.4754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3498 Z= 0.103 Angle : 0.638 11.307 4779 Z= 0.355 Chirality : 0.109 1.401 603 Planarity : 0.003 0.038 573 Dihedral : 5.577 33.569 702 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.04 % Favored : 83.96 % Rotamer: Outliers : 5.56 % Allowed : 33.33 % Favored : 61.11 % 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: -5.31 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 180 TYR 0.015 0.001 TYR B 143 PHE 0.005 0.001 PHE C 237 HIS 0.002 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 3483) covalent geometry : angle 0.62772 ( 4737) SS BOND : bond 0.00010 ( 3) SS BOND : angle 0.39577 ( 6) hydrogen bonds : bond 0.03189 ( 24) hydrogen bonds : angle 5.26002 ( 72) link_NAG-ASN : bond 0.00187 ( 12) link_NAG-ASN : angle 1.48324 ( 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 114 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: B 182 ASN cc_start: 0.8189 (t0) cc_final: 0.7986 (t0) REVERT: B 207 MET cc_start: 0.5823 (tpt) cc_final: 0.5590 (tmm) REVERT: B 241 GLU cc_start: 0.7968 (tt0) cc_final: 0.7654 (tt0) REVERT: A 132 TYR cc_start: 0.8684 (t80) cc_final: 0.8355 (t80) REVERT: A 168 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: A 207 MET cc_start: 0.5959 (tmt) cc_final: 0.5723 (tmm) REVERT: A 239 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.7315 (p-80) REVERT: A 247 ARG cc_start: 0.7691 (mtm-85) cc_final: 0.5964 (mtp85) REVERT: C 124 LYS cc_start: 0.8578 (mptm) cc_final: 0.7422 (mmtt) REVERT: C 132 TYR cc_start: 0.7783 (t80) cc_final: 0.7577 (t80) REVERT: C 150 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8247 (mt) REVERT: C 163 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: C 178 LYS cc_start: 0.7516 (ptmm) cc_final: 0.6827 (pttt) REVERT: C 207 MET cc_start: 0.6939 (tmt) cc_final: 0.6364 (tmm) REVERT: C 215 THR cc_start: 0.7145 (p) cc_final: 0.6725 (t) REVERT: C 250 TYR cc_start: 0.8049 (p90) cc_final: 0.4676 (t80) outliers start: 21 outliers final: 9 residues processed: 107 average time/residue: 0.6063 time to fit residues: 67.9893 Evaluate side-chains 102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 163 GLU 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 150 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN A 155 ASN A 242 GLN C 154 ASN C 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.206704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.187975 restraints weight = 12169.515| |-----------------------------------------------------------------------------| r_work (start): 0.4772 rms_B_bonded: 2.04 r_work: 0.4716 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4645 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.4645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.7121 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= 0.160 Angle : 0.688 11.488 4779 Z= 0.381 Chirality : 0.111 1.439 603 Planarity : 0.004 0.039 573 Dihedral : 5.646 30.147 702 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.05 % Favored : 81.95 % Rotamer: Outliers : 5.82 % Allowed : 32.54 % Favored : 61.64 % 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: -5.25 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 180 TYR 0.019 0.002 TYR B 143 PHE 0.008 0.001 PHE C 171 HIS 0.001 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 3483) covalent geometry : angle 0.67447 ( 4737) SS BOND : bond 0.00125 ( 3) SS BOND : angle 0.94002 ( 6) hydrogen bonds : bond 0.03219 ( 24) hydrogen bonds : angle 5.39862 ( 72) link_NAG-ASN : bond 0.00187 ( 12) link_NAG-ASN : angle 1.69362 ( 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 115 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 239 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7437 (p-80) REVERT: B 241 GLU cc_start: 0.7996 (tt0) cc_final: 0.7696 (tt0) REVERT: A 132 TYR cc_start: 0.8676 (t80) cc_final: 0.8334 (t80) REVERT: A 168 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: A 207 MET cc_start: 0.6175 (OUTLIER) cc_final: 0.5883 (tmm) REVERT: A 239 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7563 (p-80) REVERT: A 247 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.5921 (mtp85) REVERT: C 124 LYS cc_start: 0.8650 (mptm) cc_final: 0.7515 (mmtt) REVERT: C 150 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8481 (mt) REVERT: C 178 LYS cc_start: 0.7678 (ptmm) cc_final: 0.7013 (pttt) REVERT: C 207 MET cc_start: 0.7075 (tmt) cc_final: 0.6324 (tmm) REVERT: C 215 THR cc_start: 0.7646 (p) cc_final: 0.7004 (t) REVERT: C 239 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6829 (p-80) REVERT: C 250 TYR cc_start: 0.8321 (p90) cc_final: 0.4755 (t80) outliers start: 22 outliers final: 10 residues processed: 106 average time/residue: 0.6146 time to fit residues: 68.2485 Evaluate side-chains 105 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL 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 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 192 MET Chi-restraints excluded: chain C residue 239 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN A 148 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 = 0.4947 r_free = 0.4947 target = 0.210916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.192292 restraints weight = 12101.711| |-----------------------------------------------------------------------------| r_work (start): 0.4835 rms_B_bonded: 2.11 r_work: 0.4780 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4709 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.4709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.7255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3498 Z= 0.116 Angle : 0.665 11.406 4779 Z= 0.369 Chirality : 0.110 1.419 603 Planarity : 0.003 0.038 573 Dihedral : 5.501 29.789 702 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.79 % Favored : 83.21 % Rotamer: Outliers : 4.23 % Allowed : 34.66 % Favored : 61.11 % 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: -5.23 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 180 TYR 0.014 0.001 TYR B 143 PHE 0.006 0.001 PHE C 171 HIS 0.001 0.000 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3483) covalent geometry : angle 0.65382 ( 4737) SS BOND : bond 0.00053 ( 3) SS BOND : angle 0.53787 ( 6) hydrogen bonds : bond 0.03403 ( 24) hydrogen bonds : angle 5.31172 ( 72) link_NAG-ASN : bond 0.00156 ( 12) link_NAG-ASN : angle 1.53871 ( 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 107 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7905 (mp0) cc_final: 0.7624 (mp0) REVERT: B 207 MET cc_start: 0.7060 (tmm) cc_final: 0.6549 (tmm) REVERT: B 241 GLU cc_start: 0.7991 (tt0) cc_final: 0.7685 (tt0) REVERT: A 132 TYR cc_start: 0.8666 (t80) cc_final: 0.8320 (t80) REVERT: A 168 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: A 207 MET cc_start: 0.6425 (tmt) cc_final: 0.5842 (tmm) REVERT: A 211 TYR cc_start: 0.7424 (t80) cc_final: 0.7185 (t80) REVERT: A 239 HIS cc_start: 0.7748 (OUTLIER) cc_final: 0.7441 (p-80) REVERT: A 247 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.5849 (mtp85) REVERT: C 124 LYS cc_start: 0.8600 (mptm) cc_final: 0.7344 (mmtt) REVERT: C 150 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8531 (mt) REVERT: C 161 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6575 (mt-10) REVERT: C 178 LYS cc_start: 0.7624 (ptmm) cc_final: 0.7009 (pttt) REVERT: C 207 MET cc_start: 0.6759 (tmt) cc_final: 0.6406 (tmm) REVERT: C 215 THR cc_start: 0.7557 (p) cc_final: 0.6911 (t) REVERT: C 250 TYR cc_start: 0.8355 (p90) cc_final: 0.4760 (t80) outliers start: 16 outliers final: 10 residues processed: 101 average time/residue: 0.6496 time to fit residues: 68.8511 Evaluate side-chains 101 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 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 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 150 LEU Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN A 242 GLN C 156 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 = 0.4859 r_free = 0.4859 target = 0.202631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.184210 restraints weight = 12177.347| |-----------------------------------------------------------------------------| r_work (start): 0.4740 rms_B_bonded: 2.05 r_work: 0.4687 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4616 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.4616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.7621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3498 Z= 0.164 Angle : 0.698 11.498 4779 Z= 0.387 Chirality : 0.111 1.439 603 Planarity : 0.004 0.039 573 Dihedral : 5.669 29.606 702 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.55 % Favored : 81.45 % Rotamer: Outliers : 4.23 % Allowed : 34.66 % Favored : 61.11 % 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: -5.25 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 180 TYR 0.022 0.002 TYR C 143 PHE 0.006 0.001 PHE C 213 HIS 0.002 0.000 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 3483) covalent geometry : angle 0.68502 ( 4737) SS BOND : bond 0.00137 ( 3) SS BOND : angle 1.02173 ( 6) hydrogen bonds : bond 0.03365 ( 24) hydrogen bonds : angle 5.44171 ( 72) link_NAG-ASN : bond 0.00173 ( 12) link_NAG-ASN : angle 1.67956 ( 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 103 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 182 ASN cc_start: 0.8565 (t0) cc_final: 0.8323 (t0) REVERT: B 241 GLU cc_start: 0.8017 (tt0) cc_final: 0.7697 (tt0) REVERT: A 132 TYR cc_start: 0.8688 (t80) cc_final: 0.8319 (t80) REVERT: A 207 MET cc_start: 0.6611 (tmt) cc_final: 0.5989 (tmm) REVERT: A 211 TYR cc_start: 0.7475 (t80) cc_final: 0.7235 (t80) REVERT: A 247 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.5889 (mtp85) REVERT: C 124 LYS cc_start: 0.8640 (mptm) cc_final: 0.7417 (mmtt) REVERT: C 161 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6647 (mt-10) REVERT: C 178 LYS cc_start: 0.7753 (ptmm) cc_final: 0.7109 (pttt) REVERT: C 180 ARG cc_start: 0.7777 (ptp90) cc_final: 0.7228 (mtt90) REVERT: C 207 MET cc_start: 0.6837 (tmt) cc_final: 0.6462 (tmm) REVERT: C 215 THR cc_start: 0.7720 (p) cc_final: 0.7046 (t) REVERT: C 239 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6924 (p90) outliers start: 16 outliers final: 12 residues processed: 98 average time/residue: 0.6621 time to fit residues: 67.9333 Evaluate side-chains 98 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 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 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 192 MET Chi-restraints excluded: chain C residue 239 HIS 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: 6.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 HIS ** 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 = 0.4862 r_free = 0.4862 target = 0.201807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.183845 restraints weight = 12124.687| |-----------------------------------------------------------------------------| r_work (start): 0.4740 rms_B_bonded: 2.05 r_work: 0.4687 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4617 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.4617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.7855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3498 Z= 0.162 Angle : 0.694 11.508 4779 Z= 0.385 Chirality : 0.112 1.457 603 Planarity : 0.004 0.040 573 Dihedral : 5.705 29.611 702 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer: Outliers : 3.70 % Allowed : 35.19 % Favored : 61.11 % 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: -5.35 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 180 TYR 0.017 0.002 TYR C 143 PHE 0.006 0.001 PHE B 237 HIS 0.002 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 3483) covalent geometry : angle 0.68030 ( 4737) SS BOND : bond 0.00096 ( 3) SS BOND : angle 0.85196 ( 6) hydrogen bonds : bond 0.03461 ( 24) hydrogen bonds : angle 5.56062 ( 72) link_NAG-ASN : bond 0.00167 ( 12) link_NAG-ASN : angle 1.71721 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2953.05 seconds wall clock time: 50 minutes 36.67 seconds (3036.67 seconds total)