Starting phenix.real_space_refine on Wed Jul 23 07:55:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm2_27524/07_2025/8dm2_27524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm2_27524/07_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_27524/07_2025/8dm2_27524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm2_27524/07_2025/8dm2_27524.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm2_27524/07_2025/8dm2_27524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm2_27524/07_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-5711/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: 2.94, per 1000 atoms: 1.40 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: 0.46 Conformation dependent library (CDL) restraints added in 194.2 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: 0.29 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: 0.58 Time building geometry restraints manager: 0.55 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.910 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.630 ------------------------------------------------------------------------------- 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 : 0.231 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: 0.9102 time to fit residues: 69.0006 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 : 0.281 ------------------------------------------------------------------------------- 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: 0.6980 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.129626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.103467 restraints weight = 3539.276| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.85 r_work: 0.3226 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 2165 Z= 0.247 Angle : 0.805 10.659 2953 Z= 0.416 Chirality : 0.052 0.171 343 Planarity : 0.006 0.056 364 Dihedral : 9.780 58.418 397 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.00 % Allowed : 16.89 % 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: -0.19 (0.52), residues: 239 helix: None (None), residues: 0 sheet: 1.11 (0.47), residues: 111 loop : -1.35 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 64 HIS 0.013 0.002 HIS A 69 PHE 0.016 0.002 PHE A 133 TYR 0.016 0.002 TYR A 279 ARG 0.009 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 5) link_NAG-ASN : angle 2.16519 ( 15) link_BETA1-4 : bond 0.00081 ( 1) link_BETA1-4 : angle 1.58406 ( 3) hydrogen bonds : bond 0.03715 ( 80) hydrogen bonds : angle 6.48818 ( 213) SS BOND : bond 0.00294 ( 2) SS BOND : angle 1.89988 ( 4) covalent geometry : bond 0.00596 ( 2157) covalent geometry : angle 0.78815 ( 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 53 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.235 Fit side-chains REVERT: A 41 LYS cc_start: 0.9224 (mttm) cc_final: 0.7280 (tptt) REVERT: A 102 ARG cc_start: 0.8185 (ttm-80) cc_final: 0.7752 (mtt90) REVERT: A 153 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.6409 (mtt) REVERT: A 157 PHE cc_start: 0.8207 (m-10) cc_final: 0.7986 (m-10) REVERT: A 205 SER cc_start: 0.9087 (p) cc_final: 0.8869 (p) REVERT: A 210 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6658 (mp) REVERT: A 246 ARG cc_start: 0.6253 (mmt180) cc_final: 0.5966 (mmt180) REVERT: A 273 ARG cc_start: 0.7836 (mmt90) cc_final: 0.7524 (mtp85) outliers start: 9 outliers final: 1 residues processed: 51 average time/residue: 0.9050 time to fit residues: 47.4594 Evaluate side-chains 35 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 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 210 ILE 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: 0.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 188 ASN A 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.101080 restraints weight = 3679.348| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.83 r_work: 0.3210 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.7076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 2165 Z= 0.218 Angle : 0.703 7.791 2953 Z= 0.362 Chirality : 0.051 0.211 343 Planarity : 0.004 0.027 364 Dihedral : 8.660 56.445 397 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 6.67 % Allowed : 20.00 % Favored : 73.33 % 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: -0.47 (0.53), residues: 239 helix: None (None), residues: 0 sheet: 0.87 (0.49), residues: 106 loop : -1.38 (0.52), 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 0.011 0.002 PHE A 175 TYR 0.011 0.002 TYR A 266 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 5) link_NAG-ASN : angle 2.03239 ( 15) link_BETA1-4 : bond 0.00036 ( 1) link_BETA1-4 : angle 1.35925 ( 3) hydrogen bonds : bond 0.03621 ( 80) hydrogen bonds : angle 5.99915 ( 213) SS BOND : bond 0.01224 ( 2) SS BOND : angle 1.27411 ( 4) covalent geometry : bond 0.00526 ( 2157) covalent geometry : angle 0.68706 ( 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 49 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.239 Fit side-chains REVERT: A 41 LYS cc_start: 0.9211 (mttm) cc_final: 0.7223 (tptt) REVERT: A 102 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7884 (mmt90) REVERT: A 153 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6593 (mtt) REVERT: A 157 PHE cc_start: 0.8172 (m-10) cc_final: 0.7957 (m-10) REVERT: A 177 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6872 (mpp) REVERT: A 190 ARG cc_start: 0.8913 (ttm110) cc_final: 0.7861 (ttm-80) REVERT: A 205 SER cc_start: 0.9017 (p) cc_final: 0.8728 (p) REVERT: A 240 THR cc_start: 0.9391 (OUTLIER) cc_final: 0.8949 (t) REVERT: A 246 ARG cc_start: 0.6364 (mmt180) cc_final: 0.5909 (mmt180) outliers start: 15 outliers final: 2 residues processed: 42 average time/residue: 0.9204 time to fit residues: 39.7682 Evaluate side-chains 28 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 240 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 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 = 0.3698 r_free = 0.3698 target = 0.128244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.102776 restraints weight = 3580.071| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.81 r_work: 0.3238 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.7498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2165 Z= 0.144 Angle : 0.607 7.934 2953 Z= 0.306 Chirality : 0.047 0.200 343 Planarity : 0.003 0.023 364 Dihedral : 7.226 48.311 395 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.56 % Allowed : 25.78 % Favored : 70.67 % 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: -0.60 (0.54), residues: 239 helix: None (None), residues: 0 sheet: 0.82 (0.49), residues: 107 loop : -1.53 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.004 0.001 HIS A 69 PHE 0.008 0.001 PHE A 43 TYR 0.008 0.001 TYR A 279 ARG 0.003 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 5) link_NAG-ASN : angle 1.85282 ( 15) link_BETA1-4 : bond 0.00189 ( 1) link_BETA1-4 : angle 0.97571 ( 3) hydrogen bonds : bond 0.03122 ( 80) hydrogen bonds : angle 5.83764 ( 213) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.77492 ( 4) covalent geometry : bond 0.00340 ( 2157) covalent geometry : angle 0.59350 ( 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: 8 poor density : 30 time to evaluate : 0.186 Fit side-chains REVERT: A 41 LYS cc_start: 0.9170 (mttm) cc_final: 0.7174 (tptt) REVERT: A 153 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6649 (mtt) REVERT: A 157 PHE cc_start: 0.8155 (m-10) cc_final: 0.7916 (m-10) REVERT: A 190 ARG cc_start: 0.8704 (ttm110) cc_final: 0.8074 (ttm-80) REVERT: A 205 SER cc_start: 0.8844 (p) cc_final: 0.8527 (p) REVERT: A 246 ARG cc_start: 0.6204 (mmt180) cc_final: 0.5821 (mmt180) outliers start: 8 outliers final: 4 residues processed: 34 average time/residue: 1.3441 time to fit residues: 46.6508 Evaluate side-chains 30 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 128 ILE 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: 0.8980 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 0.0670 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.127347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.101516 restraints weight = 3726.467| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.92 r_work: 0.3215 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.7956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2165 Z= 0.158 Angle : 0.633 7.788 2953 Z= 0.321 Chirality : 0.047 0.174 343 Planarity : 0.003 0.025 364 Dihedral : 6.485 46.495 395 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.56 % Allowed : 25.78 % Favored : 70.67 % 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: -0.66 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.78 (0.51), residues: 107 loop : -1.57 (0.54), residues: 132 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 0.009 0.001 TYR A 266 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 5) link_NAG-ASN : angle 1.73898 ( 15) link_BETA1-4 : bond 0.00287 ( 1) link_BETA1-4 : angle 0.83627 ( 3) hydrogen bonds : bond 0.03264 ( 80) hydrogen bonds : angle 5.72762 ( 213) SS BOND : bond 0.00372 ( 2) SS BOND : angle 0.73222 ( 4) covalent geometry : bond 0.00381 ( 2157) covalent geometry : angle 0.62240 ( 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 36 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.256 Fit side-chains REVERT: A 41 LYS cc_start: 0.9160 (mttm) cc_final: 0.7173 (tptt) REVERT: A 153 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6928 (mtt) REVERT: A 157 PHE cc_start: 0.8112 (m-10) cc_final: 0.7888 (m-10) REVERT: A 190 ARG cc_start: 0.8920 (ttm110) cc_final: 0.8030 (ttm-80) REVERT: A 205 SER cc_start: 0.8857 (p) cc_final: 0.8551 (p) REVERT: A 240 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9140 (t) REVERT: A 246 ARG cc_start: 0.6298 (mmt180) cc_final: 0.5915 (mmt180) outliers start: 8 outliers final: 4 residues processed: 32 average time/residue: 1.2533 time to fit residues: 41.1358 Evaluate side-chains 29 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 128 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.127054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.101301 restraints weight = 3637.039| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.89 r_work: 0.3202 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.8160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2165 Z= 0.163 Angle : 0.602 7.074 2953 Z= 0.308 Chirality : 0.047 0.193 343 Planarity : 0.003 0.023 364 Dihedral : 6.004 46.838 395 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.33 % Allowed : 25.78 % Favored : 68.89 % 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: -0.66 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.64 (0.50), residues: 110 loop : -1.48 (0.55), residues: 129 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 175 TYR 0.009 0.001 TYR A 279 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 5) link_NAG-ASN : angle 1.56552 ( 15) link_BETA1-4 : bond 0.00232 ( 1) link_BETA1-4 : angle 0.84834 ( 3) hydrogen bonds : bond 0.03222 ( 80) hydrogen bonds : angle 5.69845 ( 213) SS BOND : bond 0.00387 ( 2) SS BOND : angle 0.71935 ( 4) covalent geometry : bond 0.00385 ( 2157) covalent geometry : angle 0.59228 ( 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 34 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.230 Fit side-chains REVERT: A 33 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.9093 (m) REVERT: A 41 LYS cc_start: 0.9156 (mttm) cc_final: 0.7171 (tptt) REVERT: A 52 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 153 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6918 (mtt) REVERT: A 157 PHE cc_start: 0.8109 (m-10) cc_final: 0.7894 (m-10) REVERT: A 190 ARG cc_start: 0.8689 (ttm110) cc_final: 0.8066 (ttm-80) REVERT: A 205 SER cc_start: 0.8849 (p) cc_final: 0.8534 (p) REVERT: A 240 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.9164 (t) outliers start: 12 outliers final: 4 residues processed: 31 average time/residue: 1.0942 time to fit residues: 34.8393 Evaluate side-chains 31 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 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: 0.4980 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.0040 chunk 23 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.127865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101843 restraints weight = 3741.700| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.98 r_work: 0.3221 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.8271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2165 Z= 0.137 Angle : 0.574 6.933 2953 Z= 0.295 Chirality : 0.047 0.187 343 Planarity : 0.003 0.023 364 Dihedral : 5.851 46.657 395 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.11 % Allowed : 28.00 % Favored : 68.89 % 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: -0.62 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.75 (0.52), residues: 106 loop : -1.46 (0.54), residues: 133 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 0.010 0.001 PHE A 175 TYR 0.008 0.001 TYR A 279 ARG 0.004 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 5) link_NAG-ASN : angle 1.52273 ( 15) link_BETA1-4 : bond 0.00259 ( 1) link_BETA1-4 : angle 0.95810 ( 3) hydrogen bonds : bond 0.03084 ( 80) hydrogen bonds : angle 5.60067 ( 213) SS BOND : bond 0.00304 ( 2) SS BOND : angle 0.66194 ( 4) covalent geometry : bond 0.00325 ( 2157) covalent geometry : angle 0.56471 ( 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 31 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9093 (m) REVERT: A 41 LYS cc_start: 0.9149 (mttm) cc_final: 0.7192 (tptt) REVERT: A 52 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8116 (tm-30) REVERT: A 157 PHE cc_start: 0.8116 (m-10) cc_final: 0.7907 (m-10) REVERT: A 205 SER cc_start: 0.8832 (p) cc_final: 0.8514 (p) REVERT: A 240 THR cc_start: 0.9427 (OUTLIER) cc_final: 0.9158 (t) outliers start: 7 outliers final: 5 residues processed: 28 average time/residue: 1.1445 time to fit residues: 32.9583 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 48 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 128 ILE 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: 1.9990 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.125982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099920 restraints weight = 3823.785| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 4.03 r_work: 0.3192 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.8449 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= 0.188 Angle : 0.602 7.130 2953 Z= 0.309 Chirality : 0.048 0.188 343 Planarity : 0.003 0.023 364 Dihedral : 5.998 46.625 395 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.56 % Allowed : 28.44 % 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: -0.64 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.73 (0.52), residues: 106 loop : -1.48 (0.54), 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 0.012 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 0.00270 ( 5) link_NAG-ASN : angle 1.51263 ( 15) link_BETA1-4 : bond 0.00186 ( 1) link_BETA1-4 : angle 1.09998 ( 3) hydrogen bonds : bond 0.03360 ( 80) hydrogen bonds : angle 5.64960 ( 213) SS BOND : bond 0.00452 ( 2) SS BOND : angle 0.81453 ( 4) covalent geometry : bond 0.00443 ( 2157) covalent geometry : angle 0.59285 ( 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 33 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9088 (m) REVERT: A 41 LYS cc_start: 0.9169 (mttm) cc_final: 0.7247 (tptt) REVERT: A 52 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 157 PHE cc_start: 0.8122 (m-10) cc_final: 0.7916 (m-10) REVERT: A 205 SER cc_start: 0.8852 (p) cc_final: 0.8497 (p) REVERT: A 240 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.9139 (t) outliers start: 8 outliers final: 5 residues processed: 30 average time/residue: 1.1941 time to fit residues: 36.7387 Evaluate side-chains 27 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 128 ILE 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: 0.6980 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.126173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100287 restraints weight = 3743.830| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.98 r_work: 0.3197 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.8539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2165 Z= 0.163 Angle : 0.622 6.931 2953 Z= 0.313 Chirality : 0.047 0.188 343 Planarity : 0.003 0.024 364 Dihedral : 5.903 46.538 395 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.11 % Allowed : 29.33 % Favored : 67.56 % 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: -0.73 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.51 (0.51), residues: 110 loop : -1.44 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.004 0.001 HIS A 69 PHE 0.013 0.001 PHE A 175 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 0.00183 ( 5) link_NAG-ASN : angle 1.49132 ( 15) link_BETA1-4 : bond 0.00219 ( 1) link_BETA1-4 : angle 1.03936 ( 3) hydrogen bonds : bond 0.03230 ( 80) hydrogen bonds : angle 5.61643 ( 213) SS BOND : bond 0.00356 ( 2) SS BOND : angle 0.75635 ( 4) covalent geometry : bond 0.00389 ( 2157) covalent geometry : angle 0.61364 ( 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 27 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9050 (m) REVERT: A 41 LYS cc_start: 0.9142 (mttm) cc_final: 0.7178 (tptt) REVERT: A 52 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 157 PHE cc_start: 0.8088 (m-10) cc_final: 0.7868 (m-10) REVERT: A 205 SER cc_start: 0.8822 (p) cc_final: 0.8475 (p) REVERT: A 240 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.9120 (t) REVERT: A 246 ARG cc_start: 0.6278 (mmt180) cc_final: 0.6061 (mmt180) outliers start: 7 outliers final: 4 residues processed: 25 average time/residue: 1.4224 time to fit residues: 36.3597 Evaluate side-chains 26 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 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: 0.8980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 0.0030 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.126161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.100335 restraints weight = 3717.206| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.96 r_work: 0.3193 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.8599 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= 0.155 Angle : 0.619 7.966 2953 Z= 0.311 Chirality : 0.047 0.186 343 Planarity : 0.003 0.023 364 Dihedral : 5.855 47.037 395 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.11 % Allowed : 29.33 % Favored : 67.56 % 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: -0.75 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.50 (0.51), residues: 110 loop : -1.45 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.004 0.001 HIS A 69 PHE 0.012 0.001 PHE A 175 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 0.00172 ( 5) link_NAG-ASN : angle 1.45991 ( 15) link_BETA1-4 : bond 0.00244 ( 1) link_BETA1-4 : angle 1.08175 ( 3) hydrogen bonds : bond 0.03198 ( 80) hydrogen bonds : angle 5.59723 ( 213) SS BOND : bond 0.00327 ( 2) SS BOND : angle 0.73143 ( 4) covalent geometry : bond 0.00368 ( 2157) covalent geometry : angle 0.61135 ( 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 30 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.9053 (m) REVERT: A 41 LYS cc_start: 0.9142 (mttm) cc_final: 0.7189 (tptt) REVERT: A 52 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8059 (tm-30) REVERT: A 157 PHE cc_start: 0.8092 (m-10) cc_final: 0.7876 (m-10) REVERT: A 177 MET cc_start: 0.6760 (pmm) cc_final: 0.5789 (tpp) REVERT: A 205 SER cc_start: 0.8810 (p) cc_final: 0.8458 (p) REVERT: A 240 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.9124 (t) outliers start: 7 outliers final: 2 residues processed: 27 average time/residue: 1.3563 time to fit residues: 37.4323 Evaluate side-chains 26 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 124 THR 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: 0.8980 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.126176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.100096 restraints weight = 3690.626| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.97 r_work: 0.3192 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.8659 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= 0.163 Angle : 0.617 7.733 2953 Z= 0.310 Chirality : 0.047 0.186 343 Planarity : 0.003 0.023 364 Dihedral : 5.861 47.456 395 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.11 % Allowed : 29.33 % Favored : 67.56 % 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 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.62 (0.52), residues: 106 loop : -1.55 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.004 0.001 HIS A 69 PHE 0.013 0.001 PHE A 175 TYR 0.009 0.001 TYR A 279 ARG 0.004 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 5) link_NAG-ASN : angle 1.45052 ( 15) link_BETA1-4 : bond 0.00212 ( 1) link_BETA1-4 : angle 1.09612 ( 3) hydrogen bonds : bond 0.03234 ( 80) hydrogen bonds : angle 5.58335 ( 213) SS BOND : bond 0.00354 ( 2) SS BOND : angle 0.74678 ( 4) covalent geometry : bond 0.00389 ( 2157) covalent geometry : angle 0.60854 ( 2931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2231.55 seconds wall clock time: 38 minutes 54.43 seconds (2334.43 seconds total)