Starting phenix.real_space_refine on Fri May 9 13:47:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm2_27524/05_2025/8dm2_27524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm2_27524/05_2025/8dm2_27524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm2_27524/05_2025/8dm2_27524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm2_27524/05_2025/8dm2_27524.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm2_27524/05_2025/8dm2_27524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm2_27524/05_2025/8dm2_27524.cif" } resolution = 2.91 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= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 1360 2.51 5 N 337 2.21 5 O 400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2104 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2020 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain breaks: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 Time building chain proxies: 3.28, per 1000 atoms: 1.56 Number of scatterers: 2104 At special positions: 0 Unit cell: (52, 64, 69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 7 16.00 O 400 8.00 N 337 7.00 C 1360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 423.4 milliseconds 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 474 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 51.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.712A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.983A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.723A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.56 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 631 1.34 - 1.45: 479 1.45 - 1.57: 1038 1.57 - 1.69: 0 1.69 - 1.80: 9 Bond restraints: 2157 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.77e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.37e+00 ... (remaining 2152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 2560 1.44 - 2.88: 301 2.88 - 4.32: 55 4.32 - 5.76: 12 5.76 - 7.20: 3 Bond angle restraints: 2931 Sorted by residual: angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.46 129.45 -6.99 1.41e+00 5.03e-01 2.46e+01 angle pdb=" C ALA A 292 " pdb=" N LEU A 293 " pdb=" CA LEU A 293 " ideal model delta sigma weight residual 121.70 128.33 -6.63 1.80e+00 3.09e-01 1.36e+01 angle pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " pdb=" CG ASP A 198 " ideal model delta sigma weight residual 112.60 116.03 -3.43 1.00e+00 1.00e+00 1.18e+01 angle pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 114.40 121.60 -7.20 2.30e+00 1.89e-01 9.80e+00 angle pdb=" CA TYR A 144 " pdb=" CB TYR A 144 " pdb=" CG TYR A 144 " ideal model delta sigma weight residual 113.90 118.71 -4.81 1.80e+00 3.09e-01 7.15e+00 ... (remaining 2926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 1215 16.84 - 33.68: 87 33.68 - 50.53: 21 50.53 - 67.37: 8 67.37 - 84.21: 2 Dihedral angle restraints: 1333 sinusoidal: 601 harmonic: 732 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -52.53 -33.47 1 1.00e+01 1.00e-02 1.59e+01 dihedral pdb=" C ASP A 198 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " ideal model delta harmonic sigma weight residual -122.60 -131.58 8.98 0 2.50e+00 1.60e-01 1.29e+01 dihedral pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " ideal model delta harmonic sigma weight residual 122.80 131.10 -8.30 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 1330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 236 0.062 - 0.124: 83 0.124 - 0.186: 19 0.186 - 0.248: 3 0.248 - 0.310: 2 Chirality restraints: 343 Sorted by residual: chirality pdb=" CG LEU A 249 " pdb=" CB LEU A 249 " pdb=" CD1 LEU A 249 " pdb=" CD2 LEU A 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA ASP A 198 " pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CB ASP A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE A 233 " pdb=" CA ILE A 233 " pdb=" CG1 ILE A 233 " pdb=" CG2 ILE A 233 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 340 not shown) Planarity restraints: 369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 210 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C ILE A 210 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE A 210 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN A 211 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 197 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C ILE A 197 " -0.033 2.00e-02 2.50e+03 pdb=" O ILE A 197 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP A 198 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 273 " -0.168 9.50e-02 1.11e+02 7.54e-02 3.54e+00 pdb=" NE ARG A 273 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 273 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 273 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 273 " -0.008 2.00e-02 2.50e+03 ... (remaining 366 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 747 2.87 - 3.38: 1629 3.38 - 3.88: 3434 3.88 - 4.39: 3985 4.39 - 4.90: 6978 Nonbonded interactions: 16773 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.362 3.040 nonbonded pdb=" NH1 ARG A 102 " pdb=" OE2 GLU A 154 " model vdw 2.407 3.120 nonbonded pdb=" O HIS A 245 " pdb=" N THR A 259 " model vdw 2.408 3.120 nonbonded pdb=" O5 NAG A1302 " pdb=" O6 NAG A1302 " model vdw 2.447 2.432 nonbonded pdb=" O5 NAG A1301 " pdb=" O6 NAG A1301 " model vdw 2.474 2.432 ... (remaining 16768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.670 Find NCS groups from input model: 0.020 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:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 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 : 0.007 0.044 2165 Z= 0.339 Angle : 1.042 7.202 2953 Z= 0.571 Chirality : 0.069 0.310 343 Planarity : 0.007 0.075 364 Dihedral : 13.368 84.211 853 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.44 % Allowed : 3.11 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.50), residues: 239 helix: None (None), residues: 0 sheet: 0.70 (0.44), residues: 112 loop : -1.37 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 64 HIS 0.005 0.002 HIS A 66 PHE 0.023 0.003 PHE A 175 TYR 0.019 0.003 TYR A 144 ARG 0.005 0.001 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00709 ( 5) link_NAG-ASN : angle 2.79250 ( 15) link_BETA1-4 : bond 0.01125 ( 1) link_BETA1-4 : angle 2.47550 ( 3) hydrogen bonds : bond 0.05975 ( 80) hydrogen bonds : angle 6.55212 ( 213) SS BOND : bond 0.00316 ( 2) SS BOND : angle 2.18502 ( 4) covalent geometry : bond 0.00744 ( 2157) covalent geometry : angle 1.02064 ( 2931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.6920 (mttm) cc_final: 0.5331 (tptp) REVERT: A 266 TYR cc_start: 0.8088 (m-80) cc_final: 0.7716 (m-80) outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.9179 time to fit residues: 69.6454 Evaluate side-chains 42 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.129578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.103425 restraints weight = 3542.816| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.85 r_work: 0.3221 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 2165 Z= 0.226 Angle : 0.785 10.302 2953 Z= 0.404 Chirality : 0.051 0.166 343 Planarity : 0.006 0.051 364 Dihedral : 9.764 58.568 397 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.89 % Allowed : 16.00 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.52), residues: 239 helix: None (None), residues: 0 sheet: 1.08 (0.47), residues: 111 loop : -1.29 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 64 HIS 0.005 0.001 HIS A 69 PHE 0.018 0.002 PHE A 133 TYR 0.015 0.002 TYR A 279 ARG 0.008 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 5) link_NAG-ASN : angle 2.08740 ( 15) link_BETA1-4 : bond 0.00215 ( 1) link_BETA1-4 : angle 1.61268 ( 3) hydrogen bonds : bond 0.03661 ( 80) hydrogen bonds : angle 6.52045 ( 213) SS BOND : bond 0.00480 ( 2) SS BOND : angle 1.36109 ( 4) covalent geometry : bond 0.00537 ( 2157) covalent geometry : angle 0.76983 ( 2931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9169 (mttm) cc_final: 0.7263 (tptt) REVERT: A 102 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7852 (mtt90) REVERT: A 153 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.6319 (mtt) REVERT: A 157 PHE cc_start: 0.8221 (m-10) cc_final: 0.7955 (m-10) REVERT: A 205 SER cc_start: 0.9062 (p) cc_final: 0.8844 (p) REVERT: A 246 ARG cc_start: 0.6188 (mmt180) cc_final: 0.5816 (mmt180) REVERT: A 273 ARG cc_start: 0.7760 (mmt90) cc_final: 0.7440 (mtp85) outliers start: 11 outliers final: 1 residues processed: 54 average time/residue: 0.9529 time to fit residues: 52.7554 Evaluate side-chains 35 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 153 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.101335 restraints weight = 3657.033| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.86 r_work: 0.3207 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.6902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 2165 Z= 0.223 Angle : 0.734 8.531 2953 Z= 0.373 Chirality : 0.049 0.163 343 Planarity : 0.004 0.028 364 Dihedral : 8.634 56.879 395 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.67 % Allowed : 22.22 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.53), residues: 239 helix: None (None), residues: 0 sheet: 0.83 (0.48), residues: 106 loop : -1.32 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.004 0.002 HIS A 69 PHE 0.014 0.002 PHE A 133 TYR 0.014 0.002 TYR A 266 ARG 0.004 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 5) link_NAG-ASN : angle 2.11904 ( 15) link_BETA1-4 : bond 0.00198 ( 1) link_BETA1-4 : angle 1.41466 ( 3) hydrogen bonds : bond 0.03502 ( 80) hydrogen bonds : angle 5.98766 ( 213) SS BOND : bond 0.00284 ( 2) SS BOND : angle 2.35468 ( 4) covalent geometry : bond 0.00532 ( 2157) covalent geometry : angle 0.71431 ( 2931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9200 (mttm) cc_final: 0.7228 (tptt) REVERT: A 102 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7819 (mmt90) REVERT: A 153 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6509 (mtt) REVERT: A 157 PHE cc_start: 0.8290 (m-10) cc_final: 0.8069 (m-10) REVERT: A 205 SER cc_start: 0.9033 (p) cc_final: 0.8751 (p) REVERT: A 240 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.8861 (t) REVERT: A 246 ARG cc_start: 0.6366 (mmt180) cc_final: 0.5914 (mmt180) REVERT: A 273 ARG cc_start: 0.7886 (mmt90) cc_final: 0.7665 (mtp85) outliers start: 15 outliers final: 2 residues processed: 45 average time/residue: 0.8863 time to fit residues: 41.0073 Evaluate side-chains 30 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.0010 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.101511 restraints weight = 3604.823| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.83 r_work: 0.3212 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.7419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2165 Z= 0.170 Angle : 0.645 7.748 2953 Z= 0.329 Chirality : 0.049 0.183 343 Planarity : 0.004 0.029 364 Dihedral : 7.618 49.820 395 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.11 % Allowed : 28.89 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.54), residues: 239 helix: None (None), residues: 0 sheet: 0.70 (0.49), residues: 107 loop : -1.42 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.003 0.001 HIS A 69 PHE 0.011 0.001 PHE A 133 TYR 0.009 0.001 TYR A 279 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 5) link_NAG-ASN : angle 1.99764 ( 15) link_BETA1-4 : bond 0.00272 ( 1) link_BETA1-4 : angle 1.04255 ( 3) hydrogen bonds : bond 0.03246 ( 80) hydrogen bonds : angle 5.84858 ( 213) SS BOND : bond 0.00691 ( 2) SS BOND : angle 1.62890 ( 4) covalent geometry : bond 0.00398 ( 2157) covalent geometry : angle 0.62763 ( 2931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9193 (mttm) cc_final: 0.7201 (tptt) REVERT: A 153 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6592 (mtt) REVERT: A 157 PHE cc_start: 0.8269 (m-10) cc_final: 0.8066 (m-10) REVERT: A 177 MET cc_start: 0.7220 (mpp) cc_final: 0.6868 (pmm) REVERT: A 190 ARG cc_start: 0.8681 (ttm110) cc_final: 0.7866 (ttm-80) REVERT: A 205 SER cc_start: 0.8977 (p) cc_final: 0.8651 (p) REVERT: A 246 ARG cc_start: 0.6258 (mmt180) cc_final: 0.5888 (mmt180) outliers start: 7 outliers final: 2 residues processed: 35 average time/residue: 1.2266 time to fit residues: 43.8674 Evaluate side-chains 31 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 197 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.0000 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 overall best weight: 0.3384 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.128700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.102827 restraints weight = 3659.973| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.89 r_work: 0.3229 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.7833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2165 Z= 0.124 Angle : 0.595 7.130 2953 Z= 0.299 Chirality : 0.047 0.200 343 Planarity : 0.004 0.038 364 Dihedral : 6.378 46.251 395 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.00 % Allowed : 29.33 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.68 (0.50), residues: 107 loop : -1.44 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 64 HIS 0.003 0.001 HIS A 69 PHE 0.009 0.001 PHE A 133 TYR 0.007 0.001 TYR A 144 ARG 0.007 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00123 ( 5) link_NAG-ASN : angle 1.77359 ( 15) link_BETA1-4 : bond 0.00340 ( 1) link_BETA1-4 : angle 0.76465 ( 3) hydrogen bonds : bond 0.02807 ( 80) hydrogen bonds : angle 5.68292 ( 213) SS BOND : bond 0.00499 ( 2) SS BOND : angle 1.41719 ( 4) covalent geometry : bond 0.00290 ( 2157) covalent geometry : angle 0.58124 ( 2931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9160 (mttm) cc_final: 0.7165 (tptt) REVERT: A 153 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6987 (mtt) REVERT: A 157 PHE cc_start: 0.8243 (m-10) cc_final: 0.8020 (m-10) REVERT: A 177 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6962 (pmm) REVERT: A 190 ARG cc_start: 0.8753 (ttm110) cc_final: 0.8013 (ttm-80) REVERT: A 205 SER cc_start: 0.8818 (p) cc_final: 0.8500 (p) REVERT: A 240 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.9139 (t) REVERT: A 246 ARG cc_start: 0.6167 (mmt180) cc_final: 0.5798 (mmt180) outliers start: 9 outliers final: 5 residues processed: 34 average time/residue: 1.0617 time to fit residues: 37.0568 Evaluate side-chains 32 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.101701 restraints weight = 3609.628| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.91 r_work: 0.3208 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.8001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2165 Z= 0.160 Angle : 0.622 7.682 2953 Z= 0.312 Chirality : 0.047 0.185 343 Planarity : 0.003 0.031 364 Dihedral : 6.141 46.548 395 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.89 % Allowed : 28.44 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.77 (0.50), residues: 106 loop : -1.52 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.003 0.001 HIS A 69 PHE 0.010 0.001 PHE A 175 TYR 0.009 0.001 TYR A 279 ARG 0.005 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 5) link_NAG-ASN : angle 1.70996 ( 15) link_BETA1-4 : bond 0.00390 ( 1) link_BETA1-4 : angle 0.84197 ( 3) hydrogen bonds : bond 0.03061 ( 80) hydrogen bonds : angle 5.59573 ( 213) SS BOND : bond 0.00601 ( 2) SS BOND : angle 1.37132 ( 4) covalent geometry : bond 0.00381 ( 2157) covalent geometry : angle 0.60988 ( 2931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.216 Fit side-chains REVERT: A 33 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9087 (m) REVERT: A 41 LYS cc_start: 0.9162 (mttm) cc_final: 0.7221 (tptt) REVERT: A 153 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6974 (mtt) REVERT: A 157 PHE cc_start: 0.8266 (m-10) cc_final: 0.8048 (m-10) REVERT: A 177 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6919 (pmm) REVERT: A 190 ARG cc_start: 0.8743 (ttm110) cc_final: 0.8011 (ttm-80) REVERT: A 205 SER cc_start: 0.8839 (p) cc_final: 0.8534 (p) REVERT: A 240 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.9130 (t) REVERT: A 246 ARG cc_start: 0.6229 (mmt180) cc_final: 0.5820 (mmt180) outliers start: 11 outliers final: 4 residues processed: 35 average time/residue: 1.1431 time to fit residues: 40.9813 Evaluate side-chains 30 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.127231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.100915 restraints weight = 3726.083| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.98 r_work: 0.3197 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.8283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2165 Z= 0.178 Angle : 0.653 9.259 2953 Z= 0.327 Chirality : 0.048 0.190 343 Planarity : 0.003 0.032 364 Dihedral : 6.019 45.941 395 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.78 % Allowed : 28.00 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.71 (0.50), residues: 106 loop : -1.51 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 258 HIS 0.004 0.001 HIS A 69 PHE 0.011 0.001 PHE A 175 TYR 0.010 0.001 TYR A 279 ARG 0.004 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 5) link_NAG-ASN : angle 1.69138 ( 15) link_BETA1-4 : bond 0.00439 ( 1) link_BETA1-4 : angle 0.99627 ( 3) hydrogen bonds : bond 0.03183 ( 80) hydrogen bonds : angle 5.63445 ( 213) SS BOND : bond 0.00660 ( 2) SS BOND : angle 1.37486 ( 4) covalent geometry : bond 0.00419 ( 2157) covalent geometry : angle 0.64115 ( 2931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 23 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9321 (OUTLIER) cc_final: 0.9104 (m) REVERT: A 41 LYS cc_start: 0.9156 (mttm) cc_final: 0.7211 (tptt) REVERT: A 52 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8150 (tm-30) REVERT: A 153 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6849 (mtt) REVERT: A 157 PHE cc_start: 0.8288 (m-10) cc_final: 0.8078 (m-10) REVERT: A 205 SER cc_start: 0.8895 (p) cc_final: 0.8575 (p) REVERT: A 240 THR cc_start: 0.9376 (OUTLIER) cc_final: 0.9153 (t) outliers start: 13 outliers final: 6 residues processed: 34 average time/residue: 1.0846 time to fit residues: 37.8383 Evaluate side-chains 31 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.126193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100003 restraints weight = 3737.458| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.96 r_work: 0.3185 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.8435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2165 Z= 0.200 Angle : 0.679 9.397 2953 Z= 0.340 Chirality : 0.049 0.191 343 Planarity : 0.004 0.031 364 Dihedral : 6.057 45.944 395 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.56 % Allowed : 29.78 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.64 (0.50), residues: 106 loop : -1.56 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.004 0.002 HIS A 207 PHE 0.013 0.001 PHE A 175 TYR 0.011 0.001 TYR A 279 ARG 0.004 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 5) link_NAG-ASN : angle 1.69143 ( 15) link_BETA1-4 : bond 0.00365 ( 1) link_BETA1-4 : angle 1.04937 ( 3) hydrogen bonds : bond 0.03275 ( 80) hydrogen bonds : angle 5.65374 ( 213) SS BOND : bond 0.00684 ( 2) SS BOND : angle 1.36244 ( 4) covalent geometry : bond 0.00470 ( 2157) covalent geometry : angle 0.66806 ( 2931) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9093 (m) REVERT: A 41 LYS cc_start: 0.9161 (mttm) cc_final: 0.7202 (tptt) REVERT: A 52 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8086 (tm-30) REVERT: A 153 MET cc_start: 0.7041 (mtp) cc_final: 0.6836 (mtt) REVERT: A 157 PHE cc_start: 0.8315 (m-10) cc_final: 0.8100 (m-10) REVERT: A 205 SER cc_start: 0.8891 (p) cc_final: 0.8560 (p) REVERT: A 240 THR cc_start: 0.9420 (OUTLIER) cc_final: 0.9143 (t) outliers start: 8 outliers final: 5 residues processed: 31 average time/residue: 1.2464 time to fit residues: 39.5516 Evaluate side-chains 30 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 3 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.101687 restraints weight = 3641.379| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.94 r_work: 0.3195 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.8575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2165 Z= 0.150 Angle : 0.646 8.880 2953 Z= 0.323 Chirality : 0.048 0.191 343 Planarity : 0.003 0.033 364 Dihedral : 5.854 46.430 395 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.00 % Allowed : 29.78 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.46 (0.49), residues: 110 loop : -1.47 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 64 HIS 0.003 0.001 HIS A 69 PHE 0.010 0.001 PHE A 175 TYR 0.008 0.001 TYR A 144 ARG 0.004 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 5) link_NAG-ASN : angle 1.66285 ( 15) link_BETA1-4 : bond 0.00419 ( 1) link_BETA1-4 : angle 0.99764 ( 3) hydrogen bonds : bond 0.03045 ( 80) hydrogen bonds : angle 5.58188 ( 213) SS BOND : bond 0.00559 ( 2) SS BOND : angle 1.31989 ( 4) covalent geometry : bond 0.00356 ( 2157) covalent geometry : angle 0.63468 ( 2931) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9070 (m) REVERT: A 41 LYS cc_start: 0.9147 (mttm) cc_final: 0.7188 (tptt) REVERT: A 52 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 153 MET cc_start: 0.7218 (mtp) cc_final: 0.7008 (mtt) REVERT: A 157 PHE cc_start: 0.8294 (m-10) cc_final: 0.8066 (m-10) REVERT: A 177 MET cc_start: 0.6565 (pmm) cc_final: 0.5675 (tpp) REVERT: A 205 SER cc_start: 0.8866 (p) cc_final: 0.8531 (p) REVERT: A 240 THR cc_start: 0.9424 (OUTLIER) cc_final: 0.9152 (t) outliers start: 9 outliers final: 5 residues processed: 34 average time/residue: 1.1583 time to fit residues: 40.2942 Evaluate side-chains 30 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 0.0040 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.126533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.100843 restraints weight = 3619.492| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.87 r_work: 0.3183 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.8637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2165 Z= 0.181 Angle : 0.671 9.242 2953 Z= 0.333 Chirality : 0.049 0.188 343 Planarity : 0.003 0.033 364 Dihedral : 5.966 46.603 395 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.00 % Allowed : 30.22 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.57 (0.50), residues: 106 loop : -1.60 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 258 HIS 0.003 0.001 HIS A 69 PHE 0.014 0.001 PHE A 175 TYR 0.010 0.001 TYR A 279 ARG 0.004 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 5) link_NAG-ASN : angle 1.65266 ( 15) link_BETA1-4 : bond 0.00375 ( 1) link_BETA1-4 : angle 1.09389 ( 3) hydrogen bonds : bond 0.03223 ( 80) hydrogen bonds : angle 5.61919 ( 213) SS BOND : bond 0.00617 ( 2) SS BOND : angle 1.35828 ( 4) covalent geometry : bond 0.00430 ( 2157) covalent geometry : angle 0.66063 ( 2931) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.9074 (m) REVERT: A 41 LYS cc_start: 0.9158 (mttm) cc_final: 0.7231 (tptt) REVERT: A 52 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 157 PHE cc_start: 0.8286 (m-10) cc_final: 0.8068 (m-10) REVERT: A 177 MET cc_start: 0.6517 (pmm) cc_final: 0.5609 (tpp) REVERT: A 205 SER cc_start: 0.8903 (p) cc_final: 0.8562 (p) REVERT: A 240 THR cc_start: 0.9417 (OUTLIER) cc_final: 0.9142 (t) outliers start: 9 outliers final: 5 residues processed: 31 average time/residue: 1.2218 time to fit residues: 38.7662 Evaluate side-chains 30 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.125809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.099479 restraints weight = 3684.891| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.96 r_work: 0.3184 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.8737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 2165 Z= 0.215 Angle : 0.696 9.378 2953 Z= 0.346 Chirality : 0.049 0.189 343 Planarity : 0.004 0.033 364 Dihedral : 6.141 46.811 395 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.00 % Allowed : 29.78 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.46 (0.49), residues: 106 loop : -1.65 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.004 0.002 HIS A 69 PHE 0.014 0.001 PHE A 175 TYR 0.011 0.002 TYR A 279 ARG 0.008 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 5) link_NAG-ASN : angle 1.67250 ( 15) link_BETA1-4 : bond 0.00369 ( 1) link_BETA1-4 : angle 1.12331 ( 3) hydrogen bonds : bond 0.03387 ( 80) hydrogen bonds : angle 5.73126 ( 213) SS BOND : bond 0.00711 ( 2) SS BOND : angle 1.36975 ( 4) covalent geometry : bond 0.00508 ( 2157) covalent geometry : angle 0.68523 ( 2931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2062.56 seconds wall clock time: 36 minutes 20.48 seconds (2180.48 seconds total)