Starting phenix.real_space_refine on Thu Jun 5 22:27:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u15_26278/06_2025/7u15_26278.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u15_26278/06_2025/7u15_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_26278/06_2025/7u15_26278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u15_26278/06_2025/7u15_26278.map" model { file = "/net/cci-nas-00/data/ceres_data/7u15_26278/06_2025/7u15_26278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u15_26278/06_2025/7u15_26278.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6684 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" 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: "A" 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: C, B Time building chain proxies: 3.83, per 1000 atoms: 0.57 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 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: 1.59 Conformation dependent library (CDL) restraints added in 557.8 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: 0.58 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: 1.98 Time building geometry restraints manager: 1.95 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: 2811 16.15 - 32.31: 408 32.31 - 48.46: 66 48.46 - 64.61: 54 64.61 - 80.77: 15 Dihedral angle restraints: 3354 sinusoidal: 1923 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 3351 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: 485 2.19 - 2.79: 13507 2.79 - 3.40: 17853 3.40 - 4.00: 24411 4.00 - 4.60: 34874 Nonbonded interactions: 91130 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 91125 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.680 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:16.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.520 ------------------------------------------------------------------------------- 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 3496 Z= 0.299 Angle : 1.294 17.194 4775 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 : 12.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.011 0.004 HIS C 239 PHE 0.006 0.001 PHE B 237 TYR 0.028 0.003 TYR A 250 ARG 0.007 0.002 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 12) link_NAG-ASN : angle 5.21103 ( 36) hydrogen bonds : bond 0.19149 ( 24) hydrogen bonds : angle 9.36521 ( 72) SS BOND : bond 0.00079 ( 1) SS BOND : angle 0.80208 ( 2) covalent geometry : bond 0.00630 ( 3483) covalent geometry : angle 1.21659 ( 4737) *********************** 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 : 0.525 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: 0.5314 (tmm) REVERT: A 124 LYS cc_start: 0.8111 (tppt) cc_final: 0.6240 (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: 0.6287 (p0) REVERT: C 180 ARG cc_start: 0.7526 (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: 1.4060 time to fit residues: 136.9462 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 : 0.489 ------------------------------------------------------------------------------- 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 32 optimal weight: 0.0870 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- 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 B 242 GLN A 154 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN C 154 ASN C 155 ASN C 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.237442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.219534 restraints weight = 12620.423| |-----------------------------------------------------------------------------| r_work (start): 0.5015 rms_B_bonded: 2.17 r_work: 0.4965 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4900 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3496 Z= 0.148 Angle : 0.760 11.607 4775 Z= 0.418 Chirality : 0.112 1.507 603 Planarity : 0.005 0.050 573 Dihedral : 9.121 57.296 719 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.54 % Favored : 82.46 % Rotamer: Outliers : 6.35 % Allowed : 29.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.18 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.71 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS B 239 PHE 0.013 0.002 PHE C 213 TYR 0.024 0.002 TYR B 250 ARG 0.004 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 12) link_NAG-ASN : angle 1.37134 ( 36) hydrogen bonds : bond 0.04630 ( 24) hydrogen bonds : angle 7.17869 ( 72) SS BOND : bond 0.00442 ( 1) SS BOND : angle 1.92167 ( 2) covalent geometry : bond 0.00335 ( 3483) covalent geometry : angle 0.75273 ( 4737) *********************** 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 111 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.5950 (tmt) cc_final: 0.5353 (tmm) REVERT: B 241 GLU cc_start: 0.8086 (tt0) cc_final: 0.7866 (tt0) REVERT: A 124 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.5988 (pptt) REVERT: A 157 TYR cc_start: 0.8681 (m-80) cc_final: 0.8381 (m-80) REVERT: A 163 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: A 168 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7644 (tp-100) REVERT: A 178 LYS cc_start: 0.7367 (ptmm) cc_final: 0.5078 (mmmt) REVERT: A 180 ARG cc_start: 0.7457 (ptp90) cc_final: 0.6648 (mmp-170) REVERT: A 207 MET cc_start: 0.5560 (tmt) cc_final: 0.5026 (tmm) REVERT: A 247 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.6106 (mtp180) REVERT: C 150 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7310 (mt) REVERT: C 180 ARG cc_start: 0.7789 (ptp90) cc_final: 0.6479 (ptt90) REVERT: C 207 MET cc_start: 0.6567 (tmt) cc_final: 0.6024 (tmm) REVERT: C 227 MET cc_start: 0.8531 (mtm) cc_final: 0.8241 (mtm) outliers start: 24 outliers final: 4 residues processed: 101 average time/residue: 1.7324 time to fit residues: 181.8274 Evaluate side-chains 85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 163 GLU Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 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 = 0.5026 r_free = 0.5026 target = 0.222012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.203073 restraints weight = 12370.512| |-----------------------------------------------------------------------------| r_work (start): 0.4887 rms_B_bonded: 2.06 r_work: 0.4834 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4767 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3496 Z= 0.167 Angle : 0.758 11.531 4775 Z= 0.417 Chirality : 0.113 1.454 603 Planarity : 0.005 0.046 573 Dihedral : 6.779 34.774 703 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.29 % Favored : 84.71 % Rotamer: Outliers : 6.88 % Allowed : 26.98 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.83 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.43 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.008 0.002 PHE B 213 TYR 0.013 0.002 TYR A 211 ARG 0.008 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 12) link_NAG-ASN : angle 1.66935 ( 36) hydrogen bonds : bond 0.04264 ( 24) hydrogen bonds : angle 6.21488 ( 72) SS BOND : bond 0.00293 ( 1) SS BOND : angle 1.17779 ( 2) covalent geometry : bond 0.00374 ( 3483) covalent geometry : angle 0.74710 ( 4737) *********************** 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 124 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: B 178 LYS cc_start: 0.7034 (ptmm) cc_final: 0.6828 (ptmt) REVERT: B 202 VAL cc_start: 0.7114 (OUTLIER) cc_final: 0.6723 (m) REVERT: B 207 MET cc_start: 0.5914 (tmt) cc_final: 0.5652 (tpt) REVERT: B 241 GLU cc_start: 0.8055 (tt0) cc_final: 0.7819 (tt0) REVERT: A 124 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.5875 (pptt) REVERT: A 180 ARG cc_start: 0.7596 (ptp90) cc_final: 0.6418 (mmm160) REVERT: A 207 MET cc_start: 0.6198 (tmt) cc_final: 0.5720 (tmt) REVERT: A 247 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.5940 (mtp85) REVERT: C 150 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7933 (mt) REVERT: C 163 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: C 178 LYS cc_start: 0.7016 (ptmm) cc_final: 0.6714 (mtmm) REVERT: C 180 ARG cc_start: 0.8029 (ptp90) cc_final: 0.6783 (ptt90) REVERT: C 207 MET cc_start: 0.6718 (tmt) cc_final: 0.6286 (tmm) REVERT: C 227 MET cc_start: 0.8636 (mtm) cc_final: 0.8222 (mtm) REVERT: C 250 TYR cc_start: 0.7563 (p90) cc_final: 0.5060 (t80) outliers start: 26 outliers final: 10 residues processed: 116 average time/residue: 1.4612 time to fit residues: 177.2651 Evaluate side-chains 101 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 202 VAL 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 218 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 144 LEU 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 19 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 37 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 GLN ** 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 = 0.5064 r_free = 0.5064 target = 0.226808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.208503 restraints weight = 12613.239| |-----------------------------------------------------------------------------| r_work (start): 0.4944 rms_B_bonded: 2.12 r_work: 0.4894 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4824 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3496 Z= 0.103 Angle : 0.647 11.335 4775 Z= 0.360 Chirality : 0.110 1.415 603 Planarity : 0.003 0.040 573 Dihedral : 6.067 36.241 703 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.79 % Favored : 83.21 % Rotamer: Outliers : 5.29 % Allowed : 30.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.62 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.014 0.001 PHE A 213 TYR 0.011 0.001 TYR C 143 ARG 0.005 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 12) link_NAG-ASN : angle 1.45404 ( 36) hydrogen bonds : bond 0.03448 ( 24) hydrogen bonds : angle 5.78297 ( 72) SS BOND : bond 0.00374 ( 1) SS BOND : angle 1.36601 ( 2) covalent geometry : bond 0.00236 ( 3483) covalent geometry : angle 0.63615 ( 4737) *********************** 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 108 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.496 Fit side-chains REVERT: B 207 MET cc_start: 0.5980 (tmt) cc_final: 0.5661 (tpt) REVERT: B 241 GLU cc_start: 0.8023 (tt0) cc_final: 0.7770 (tt0) REVERT: A 124 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.5418 (pptt) REVERT: A 180 ARG cc_start: 0.7507 (ptp90) cc_final: 0.6263 (mmm160) REVERT: A 207 MET cc_start: 0.5963 (tmt) cc_final: 0.5480 (tmt) REVERT: A 239 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.7746 (p-80) REVERT: A 247 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.5965 (mtp85) REVERT: C 150 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7736 (mt) REVERT: C 163 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: C 178 LYS cc_start: 0.7106 (ptmm) cc_final: 0.6529 (mtmt) REVERT: C 180 ARG cc_start: 0.8037 (ptp90) cc_final: 0.6722 (ptt90) REVERT: C 192 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6562 (mtt) REVERT: C 207 MET cc_start: 0.6644 (tmt) cc_final: 0.6127 (tmm) REVERT: C 215 THR cc_start: 0.7368 (p) cc_final: 0.7117 (t) REVERT: C 250 TYR cc_start: 0.7607 (p90) cc_final: 0.5018 (t80) outliers start: 20 outliers final: 7 residues processed: 101 average time/residue: 1.3786 time to fit residues: 146.0025 Evaluate side-chains 95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 144 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4998 r_free = 0.4998 target = 0.219694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.201426 restraints weight = 12332.405| |-----------------------------------------------------------------------------| r_work (start): 0.4868 rms_B_bonded: 1.99 r_work: 0.4815 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.4749 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.4749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3496 Z= 0.133 Angle : 0.674 11.379 4775 Z= 0.374 Chirality : 0.110 1.417 603 Planarity : 0.004 0.044 573 Dihedral : 5.966 34.255 703 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.04 % Favored : 82.96 % Rotamer: Outliers : 4.76 % Allowed : 31.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.46 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.009 0.001 PHE C 171 TYR 0.013 0.001 TYR C 143 ARG 0.006 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 12) link_NAG-ASN : angle 1.51763 ( 36) hydrogen bonds : bond 0.03255 ( 24) hydrogen bonds : angle 5.52741 ( 72) SS BOND : bond 0.00277 ( 1) SS BOND : angle 1.06522 ( 2) covalent geometry : bond 0.00309 ( 3483) covalent geometry : angle 0.66350 ( 4737) *********************** 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 111 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: B 207 MET cc_start: 0.6066 (tmt) cc_final: 0.5688 (tpt) REVERT: B 239 HIS cc_start: 0.8105 (OUTLIER) cc_final: 0.7277 (p-80) REVERT: B 241 GLU cc_start: 0.7911 (tt0) cc_final: 0.7638 (tt0) REVERT: A 124 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.5858 (pptt) REVERT: A 168 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: A 180 ARG cc_start: 0.7572 (ptp90) cc_final: 0.6472 (mmm160) REVERT: A 207 MET cc_start: 0.6213 (tmt) cc_final: 0.5712 (tmt) REVERT: A 239 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.7446 (p-80) REVERT: A 247 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.6040 (mtp85) REVERT: C 150 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8114 (mt) REVERT: C 163 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: C 178 LYS cc_start: 0.7532 (ptmm) cc_final: 0.6645 (pttt) REVERT: C 180 ARG cc_start: 0.8011 (ptp90) cc_final: 0.6204 (pmt-80) REVERT: C 207 MET cc_start: 0.6869 (tmt) cc_final: 0.6359 (tmm) REVERT: C 215 THR cc_start: 0.7530 (p) cc_final: 0.7114 (t) REVERT: C 250 TYR cc_start: 0.7833 (p90) cc_final: 0.4979 (t80) outliers start: 18 outliers final: 6 residues processed: 104 average time/residue: 1.4178 time to fit residues: 154.3260 Evaluate side-chains 102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 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 168 GLN Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.212196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.193596 restraints weight = 12385.787| |-----------------------------------------------------------------------------| r_work (start): 0.4812 rms_B_bonded: 2.05 r_work: 0.4758 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4687 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3496 Z= 0.141 Angle : 0.672 11.469 4775 Z= 0.372 Chirality : 0.111 1.436 603 Planarity : 0.004 0.046 573 Dihedral : 5.786 33.081 703 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.05 % Favored : 81.95 % Rotamer: Outliers : 5.82 % Allowed : 30.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.36 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 239 PHE 0.008 0.001 PHE B 213 TYR 0.014 0.001 TYR C 143 ARG 0.006 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 12) link_NAG-ASN : angle 1.67800 ( 36) hydrogen bonds : bond 0.03423 ( 24) hydrogen bonds : angle 5.45127 ( 72) SS BOND : bond 0.00403 ( 1) SS BOND : angle 1.41902 ( 2) covalent geometry : bond 0.00330 ( 3483) covalent geometry : angle 0.65774 ( 4737) *********************** 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 120 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.5838 (tpt) REVERT: B 239 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7277 (p-80) REVERT: B 241 GLU cc_start: 0.7976 (tt0) cc_final: 0.7687 (tt0) REVERT: A 124 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.5596 (pptt) REVERT: A 132 TYR cc_start: 0.8782 (t80) cc_final: 0.8246 (t80) REVERT: A 207 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.5615 (tmt) REVERT: A 239 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.7356 (p-80) REVERT: A 247 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.5986 (mtp85) REVERT: C 150 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8283 (mt) REVERT: C 163 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: C 178 LYS cc_start: 0.7573 (ptmm) cc_final: 0.6708 (pttt) REVERT: C 180 ARG cc_start: 0.8075 (ptp90) cc_final: 0.6075 (pmt-80) REVERT: C 207 MET cc_start: 0.6912 (tmt) cc_final: 0.6447 (tmm) REVERT: C 215 THR cc_start: 0.7882 (p) cc_final: 0.7227 (t) REVERT: C 250 TYR cc_start: 0.8196 (p90) cc_final: 0.4792 (t80) outliers start: 22 outliers final: 12 residues processed: 111 average time/residue: 1.2965 time to fit residues: 151.2316 Evaluate side-chains 107 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 207 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 207 MET 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 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 163 GLU 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 33 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.213313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.194979 restraints weight = 12307.944| |-----------------------------------------------------------------------------| r_work (start): 0.4834 rms_B_bonded: 2.05 r_work: 0.4780 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4709 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.4709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.6514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 3496 Z= 0.126 Angle : 0.658 11.383 4775 Z= 0.366 Chirality : 0.110 1.424 603 Planarity : 0.004 0.043 573 Dihedral : 5.686 33.881 703 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.54 % Favored : 82.46 % Rotamer: Outliers : 5.82 % Allowed : 29.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.002 0.001 HIS C 239 PHE 0.004 0.001 PHE C 171 TYR 0.013 0.001 TYR A 211 ARG 0.006 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 12) link_NAG-ASN : angle 1.54009 ( 36) hydrogen bonds : bond 0.03190 ( 24) hydrogen bonds : angle 5.40013 ( 72) SS BOND : bond 0.00238 ( 1) SS BOND : angle 0.88004 ( 2) covalent geometry : bond 0.00301 ( 3483) covalent geometry : angle 0.64641 ( 4737) *********************** 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 117 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: B 207 MET cc_start: 0.6388 (tmt) cc_final: 0.5810 (tmm) REVERT: B 241 GLU cc_start: 0.7957 (tt0) cc_final: 0.7664 (tt0) REVERT: A 132 TYR cc_start: 0.8792 (t80) cc_final: 0.8337 (t80) REVERT: A 168 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: A 180 ARG cc_start: 0.7455 (ptp90) cc_final: 0.7195 (pmm-80) REVERT: A 207 MET cc_start: 0.6407 (OUTLIER) cc_final: 0.5919 (tmm) REVERT: A 247 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.5986 (mtp85) REVERT: C 124 LYS cc_start: 0.8563 (mmtp) cc_final: 0.7479 (mmtt) REVERT: C 150 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8379 (mt) REVERT: C 163 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: C 178 LYS cc_start: 0.7655 (ptmm) cc_final: 0.6856 (pttt) REVERT: C 207 MET cc_start: 0.6958 (tmt) cc_final: 0.6425 (tmm) REVERT: C 215 THR cc_start: 0.7539 (p) cc_final: 0.7047 (t) REVERT: C 239 HIS cc_start: 0.7221 (OUTLIER) cc_final: 0.6758 (p-80) REVERT: C 250 TYR cc_start: 0.8145 (p90) cc_final: 0.4759 (t80) outliers start: 22 outliers final: 13 residues processed: 107 average time/residue: 1.3050 time to fit residues: 146.7374 Evaluate side-chains 113 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 186 ILE Chi-restraints excluded: chain B residue 210 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 207 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain C residue 144 LEU 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 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 4 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.212954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.194471 restraints weight = 12144.591| |-----------------------------------------------------------------------------| r_work (start): 0.4831 rms_B_bonded: 2.06 r_work: 0.4778 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4707 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.6783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3496 Z= 0.125 Angle : 0.656 11.401 4775 Z= 0.365 Chirality : 0.110 1.421 603 Planarity : 0.004 0.042 573 Dihedral : 5.603 33.720 703 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.30 % Favored : 81.70 % Rotamer: Outliers : 6.35 % Allowed : 30.42 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.31 (0.33), 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 HIS 0.001 0.000 HIS B 239 PHE 0.005 0.001 PHE C 171 TYR 0.012 0.001 TYR C 143 ARG 0.008 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 12) link_NAG-ASN : angle 1.51945 ( 36) hydrogen bonds : bond 0.03088 ( 24) hydrogen bonds : angle 5.40237 ( 72) SS BOND : bond 0.00305 ( 1) SS BOND : angle 0.97399 ( 2) covalent geometry : bond 0.00292 ( 3483) covalent geometry : angle 0.64466 ( 4737) *********************** 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 119 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: B 207 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.5848 (tmm) REVERT: B 239 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7441 (p-80) REVERT: B 241 GLU cc_start: 0.7936 (tt0) cc_final: 0.7672 (tt0) REVERT: A 132 TYR cc_start: 0.8776 (t80) cc_final: 0.8456 (t80) REVERT: A 168 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: A 180 ARG cc_start: 0.7324 (ptp90) cc_final: 0.6905 (pmm-80) REVERT: A 207 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5854 (tmm) REVERT: A 247 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.5976 (mtp85) REVERT: C 124 LYS cc_start: 0.8556 (mmtp) cc_final: 0.7459 (mmtt) REVERT: C 150 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8513 (mt) REVERT: C 178 LYS cc_start: 0.7695 (ptmm) cc_final: 0.6908 (pttt) REVERT: C 207 MET cc_start: 0.6954 (tmt) cc_final: 0.6421 (tmm) REVERT: C 250 TYR cc_start: 0.8172 (p90) cc_final: 0.4763 (t80) outliers start: 24 outliers final: 14 residues processed: 108 average time/residue: 1.2497 time to fit residues: 142.0301 Evaluate side-chains 111 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 210 MET 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 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 168 GLN Chi-restraints excluded: chain C residue 192 MET 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 15 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN C 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.208953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.190442 restraints weight = 12302.292| |-----------------------------------------------------------------------------| r_work (start): 0.4801 rms_B_bonded: 2.10 r_work: 0.4747 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4674 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.7136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3496 Z= 0.142 Angle : 0.666 11.430 4775 Z= 0.371 Chirality : 0.111 1.434 603 Planarity : 0.004 0.043 573 Dihedral : 5.711 33.374 703 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.79 % Favored : 82.21 % Rotamer: Outliers : 5.82 % Allowed : 31.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.29 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 239 PHE 0.004 0.001 PHE A 213 TYR 0.015 0.001 TYR C 143 ARG 0.004 0.001 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 12) link_NAG-ASN : angle 1.58477 ( 36) hydrogen bonds : bond 0.03042 ( 24) hydrogen bonds : angle 5.45479 ( 72) SS BOND : bond 0.00223 ( 1) SS BOND : angle 0.96451 ( 2) covalent geometry : bond 0.00324 ( 3483) covalent geometry : angle 0.65414 ( 4737) *********************** 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 117 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: B 207 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6267 (tmm) REVERT: B 241 GLU cc_start: 0.7969 (tt0) cc_final: 0.7675 (tt0) REVERT: A 124 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.5564 (pptt) REVERT: A 132 TYR cc_start: 0.8816 (t80) cc_final: 0.8543 (t80) REVERT: A 168 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: A 180 ARG cc_start: 0.7347 (ptp90) cc_final: 0.6958 (pmm-80) REVERT: A 207 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.5879 (tmm) REVERT: A 247 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.5976 (mtp85) REVERT: C 124 LYS cc_start: 0.8530 (mmtp) cc_final: 0.7451 (mmtt) REVERT: C 178 LYS cc_start: 0.7764 (ptmm) cc_final: 0.6998 (pttt) REVERT: C 207 MET cc_start: 0.7033 (tmt) cc_final: 0.6466 (tmm) REVERT: C 250 TYR cc_start: 0.8344 (p90) cc_final: 0.4697 (t80) outliers start: 22 outliers final: 11 residues processed: 106 average time/residue: 1.3879 time to fit residues: 155.2728 Evaluate side-chains 110 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 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 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 192 MET 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 25 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 154 ASN C 148 ASN C 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.212781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.194778 restraints weight = 12164.582| |-----------------------------------------------------------------------------| r_work (start): 0.4852 rms_B_bonded: 2.08 r_work: 0.4795 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4723 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3496 Z= 0.113 Angle : 0.650 11.401 4775 Z= 0.362 Chirality : 0.110 1.424 603 Planarity : 0.004 0.043 573 Dihedral : 5.512 33.696 703 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.29 % Favored : 83.71 % Rotamer: Outliers : 4.23 % Allowed : 32.28 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.26 (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 HIS 0.005 0.001 HIS C 239 PHE 0.004 0.001 PHE B 171 TYR 0.014 0.001 TYR A 143 ARG 0.004 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 12) link_NAG-ASN : angle 1.52012 ( 36) hydrogen bonds : bond 0.03161 ( 24) hydrogen bonds : angle 5.43468 ( 72) SS BOND : bond 0.00174 ( 1) SS BOND : angle 0.68308 ( 2) covalent geometry : bond 0.00262 ( 3483) covalent geometry : angle 0.63872 ( 4737) ********************** 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 108 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: B 207 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6278 (tmm) REVERT: B 241 GLU cc_start: 0.7935 (tt0) cc_final: 0.7624 (tt0) REVERT: A 124 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.5331 (pptt) REVERT: A 132 TYR cc_start: 0.8828 (t80) cc_final: 0.8566 (t80) REVERT: A 168 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: A 180 ARG cc_start: 0.7316 (ptp90) cc_final: 0.6939 (pmm-80) REVERT: A 207 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.5866 (tmm) REVERT: A 239 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7393 (p-80) REVERT: A 247 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.5966 (mtp85) REVERT: C 124 LYS cc_start: 0.8427 (mmtp) cc_final: 0.7259 (mmtt) REVERT: C 178 LYS cc_start: 0.7747 (ptmm) cc_final: 0.7015 (pttt) REVERT: C 207 MET cc_start: 0.7016 (tmt) cc_final: 0.6455 (tmm) REVERT: C 215 THR cc_start: 0.7118 (p) cc_final: 0.6585 (t) REVERT: C 250 TYR cc_start: 0.8253 (p90) cc_final: 0.4743 (t80) outliers start: 16 outliers final: 9 residues processed: 98 average time/residue: 1.8711 time to fit residues: 192.9395 Evaluate side-chains 104 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE 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 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 239 HIS Chi-restraints excluded: chain C residue 192 MET 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 15 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.214944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.196848 restraints weight = 12175.066| |-----------------------------------------------------------------------------| r_work (start): 0.4867 rms_B_bonded: 2.16 r_work: 0.4812 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4741 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.4741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.7364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3496 Z= 0.106 Angle : 0.633 11.374 4775 Z= 0.354 Chirality : 0.110 1.426 603 Planarity : 0.004 0.041 573 Dihedral : 5.374 32.352 703 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.54 % Favored : 83.46 % Rotamer: Outliers : 4.23 % Allowed : 32.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.24 (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 HIS 0.005 0.001 HIS C 239 PHE 0.006 0.001 PHE A 213 TYR 0.013 0.001 TYR C 211 ARG 0.004 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 12) link_NAG-ASN : angle 1.46378 ( 36) hydrogen bonds : bond 0.03061 ( 24) hydrogen bonds : angle 5.37592 ( 72) SS BOND : bond 0.00165 ( 1) SS BOND : angle 0.50994 ( 2) covalent geometry : bond 0.00245 ( 3483) covalent geometry : angle 0.62273 ( 4737) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6132.88 seconds wall clock time: 105 minutes 51.81 seconds (6351.81 seconds total)