Starting phenix.real_space_refine on Fri May 9 21:36:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bj2_44627/05_2025/9bj2_44627.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bj2_44627/05_2025/9bj2_44627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bj2_44627/05_2025/9bj2_44627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bj2_44627/05_2025/9bj2_44627.map" model { file = "/net/cci-nas-00/data/ceres_data/9bj2_44627/05_2025/9bj2_44627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bj2_44627/05_2025/9bj2_44627.cif" } resolution = 2.8 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= 0.044 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 13 5.16 5 C 2498 2.51 5 N 651 2.21 5 O 758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3920 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2107 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 991 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 124} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 780 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N SER H 131 " occ=0.58 ... (4 atoms not shown) pdb=" OG SER H 131 " occ=0.58 Time building chain proxies: 4.35, per 1000 atoms: 1.11 Number of scatterers: 3920 At special positions: 0 Unit cell: (76.689, 83.5058, 105.66, 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 13 16.00 O 758 8.00 N 651 7.00 C 2498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 122 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 439.1 milliseconds 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 11 sheets defined 7.0% alpha, 45.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'H' and resid 25 through 31 removed outlier: 3.528A pdb=" N PHE H 29 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 4.009A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 102 through 109 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.216A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.051A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.579A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 154 removed outlier: 6.525A pdb=" N TYR A 145 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.759A pdb=" N GLU H 10 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.759A pdb=" N GLU H 10 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL H 120 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.764A pdb=" N GLY L 13 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.574A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 147 hydrogen bonds defined for protein. 372 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 1.01 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: 1241 1.34 - 1.46: 1002 1.46 - 1.58: 1760 1.58 - 1.70: 0 1.70 - 1.81: 16 Bond restraints: 4019 Sorted by residual: bond pdb=" C SER A 172 " pdb=" N GLN A 173 " ideal model delta sigma weight residual 1.331 1.367 -0.036 2.83e-02 1.25e+03 1.61e+00 bond pdb=" N ASN A 99 " pdb=" CA ASN A 99 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.45e+00 bond pdb=" CB ASN A 99 " pdb=" CG ASN A 99 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.54e-01 bond pdb=" C ILE H 52 " pdb=" O ILE H 52 " ideal model delta sigma weight residual 1.232 1.240 -0.008 1.01e-02 9.80e+03 6.60e-01 bond pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.67e-01 ... (remaining 4014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.84: 5047 0.84 - 1.68: 332 1.68 - 2.51: 56 2.51 - 3.35: 28 3.35 - 4.19: 10 Bond angle restraints: 5473 Sorted by residual: angle pdb=" N CYS A 131 " pdb=" CA CYS A 131 " pdb=" C CYS A 131 " ideal model delta sigma weight residual 108.60 104.41 4.19 1.46e+00 4.69e-01 8.24e+00 angle pdb=" N TRP H 113 " pdb=" CA TRP H 113 " pdb=" CB TRP H 113 " ideal model delta sigma weight residual 111.20 107.08 4.12 1.65e+00 3.67e-01 6.25e+00 angle pdb=" N ASN L 50 " pdb=" CA ASN L 50 " pdb=" C ASN L 50 " ideal model delta sigma weight residual 112.24 109.47 2.77 1.28e+00 6.10e-01 4.70e+00 angle pdb=" C ILE A 233 " pdb=" N ASN A 234 " pdb=" CA ASN A 234 " ideal model delta sigma weight residual 121.50 124.56 -3.06 1.43e+00 4.89e-01 4.59e+00 angle pdb=" C ASN A 148 " pdb=" CA ASN A 148 " pdb=" CB ASN A 148 " ideal model delta sigma weight residual 109.53 113.12 -3.59 1.69e+00 3.50e-01 4.51e+00 ... (remaining 5468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 2077 17.46 - 34.92: 218 34.92 - 52.39: 63 52.39 - 69.85: 11 69.85 - 87.31: 4 Dihedral angle restraints: 2373 sinusoidal: 937 harmonic: 1436 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 -129.75 43.75 1 1.00e+01 1.00e-02 2.66e+01 dihedral pdb=" CA ASN A 165 " pdb=" C ASN A 165 " pdb=" N CYS A 166 " pdb=" CA CYS A 166 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA VAL A 130 " pdb=" C VAL A 130 " pdb=" N CYS A 131 " pdb=" CA CYS A 131 " ideal model delta harmonic sigma weight residual -180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 499 0.054 - 0.107: 85 0.107 - 0.161: 28 0.161 - 0.214: 0 0.214 - 0.268: 1 Chirality restraints: 613 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE A 105 " pdb=" N ILE A 105 " pdb=" C ILE A 105 " pdb=" CB ILE A 105 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ASN A 99 " pdb=" N ASN A 99 " pdb=" C ASN A 99 " pdb=" CB ASN A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 610 not shown) Planarity restraints: 702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.025 2.00e-02 2.50e+03 2.27e-02 6.44e+00 pdb=" CG ASN A 234 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 295 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 50 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ASN L 50 " -0.023 2.00e-02 2.50e+03 pdb=" O ASN L 50 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN L 51 " 0.008 2.00e-02 2.50e+03 ... (remaining 699 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 326 2.75 - 3.29: 3305 3.29 - 3.82: 6087 3.82 - 4.36: 7425 4.36 - 4.90: 13596 Nonbonded interactions: 30739 Sorted by model distance: nonbonded pdb=" O GLY H 115 " pdb=" OH TYR L 36 " model vdw 2.208 3.040 nonbonded pdb=" O SER A 98 " pdb=" OG SER A 98 " model vdw 2.259 3.040 nonbonded pdb=" OE1 GLN L 7 " pdb=" OG1 THR L 102 " model vdw 2.261 3.040 nonbonded pdb=" O THR A 95 " pdb=" OG1 THR A 95 " model vdw 2.342 3.040 nonbonded pdb=" OH TYR A 144 " pdb=" OD2 ASP H 102 " model vdw 2.345 3.040 ... (remaining 30734 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=0.58 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: 8.370 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.380 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.002 0.036 4027 Z= 0.108 Angle : 0.541 8.214 5492 Z= 0.290 Chirality : 0.047 0.268 613 Planarity : 0.004 0.041 699 Dihedral : 15.672 87.309 1440 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.60 % Allowed : 19.86 % Favored : 77.54 % 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: 0.22 (0.38), residues: 487 helix: 0.76 (0.94), residues: 23 sheet: 1.07 (0.38), residues: 198 loop : -0.64 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 107 HIS 0.003 0.001 HIS A 66 PHE 0.011 0.001 PHE A 133 TYR 0.009 0.001 TYR A 170 ARG 0.001 0.000 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 3) link_NAG-ASN : angle 4.39365 ( 9) hydrogen bonds : bond 0.13610 ( 141) hydrogen bonds : angle 6.05291 ( 372) SS BOND : bond 0.00282 ( 5) SS BOND : angle 1.38677 ( 10) covalent geometry : bond 0.00223 ( 4019) covalent geometry : angle 0.50884 ( 5473) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.442 Fit side-chains REVERT: H 32 ASN cc_start: 0.8940 (m110) cc_final: 0.8548 (m-40) outliers start: 11 outliers final: 10 residues processed: 50 average time/residue: 0.8972 time to fit residues: 47.0879 Evaluate side-chains 45 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain L residue 19 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.0050 chunk 36 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS H 6 GLN L 7 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.161492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.126763 restraints weight = 4175.022| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.83 r_work: 0.3217 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4027 Z= 0.104 Angle : 0.519 5.627 5492 Z= 0.276 Chirality : 0.046 0.224 613 Planarity : 0.004 0.041 699 Dihedral : 6.526 59.335 617 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.55 % Allowed : 18.44 % Favored : 78.01 % 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: 0.23 (0.38), residues: 487 helix: 1.37 (0.95), residues: 23 sheet: 1.09 (0.38), residues: 200 loop : -0.72 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 107 HIS 0.003 0.001 HIS A 66 PHE 0.012 0.001 PHE A 175 TYR 0.010 0.001 TYR A 279 ARG 0.001 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 3) link_NAG-ASN : angle 2.89285 ( 9) hydrogen bonds : bond 0.03335 ( 141) hydrogen bonds : angle 5.08272 ( 372) SS BOND : bond 0.00373 ( 5) SS BOND : angle 1.08384 ( 10) covalent geometry : bond 0.00232 ( 4019) covalent geometry : angle 0.50403 ( 5473) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.403 Fit side-chains REVERT: H 32 ASN cc_start: 0.8972 (m110) cc_final: 0.8488 (m-40) REVERT: H 38 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7789 (ttm170) REVERT: H 82 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: L 96 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7972 (mp) outliers start: 15 outliers final: 6 residues processed: 49 average time/residue: 0.9139 time to fit residues: 46.9386 Evaluate side-chains 43 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 0.0670 chunk 38 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.159696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.124104 restraints weight = 4156.586| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.81 r_work: 0.3197 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4027 Z= 0.133 Angle : 0.558 6.711 5492 Z= 0.297 Chirality : 0.047 0.273 613 Planarity : 0.004 0.040 699 Dihedral : 5.178 31.296 601 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.26 % Allowed : 17.97 % Favored : 77.78 % 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: 0.20 (0.38), residues: 487 helix: 1.50 (0.94), residues: 23 sheet: 1.10 (0.38), residues: 200 loop : -0.79 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 113 HIS 0.004 0.001 HIS A 66 PHE 0.016 0.002 PHE A 175 TYR 0.012 0.001 TYR A 279 ARG 0.001 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 3) link_NAG-ASN : angle 2.51259 ( 9) hydrogen bonds : bond 0.03640 ( 141) hydrogen bonds : angle 5.00684 ( 372) SS BOND : bond 0.00601 ( 5) SS BOND : angle 2.30377 ( 10) covalent geometry : bond 0.00310 ( 4019) covalent geometry : angle 0.54057 ( 5473) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.430 Fit side-chains REVERT: H 32 ASN cc_start: 0.9096 (m110) cc_final: 0.8605 (m-40) REVERT: H 38 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7761 (ttm170) REVERT: H 51 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7726 (tp) REVERT: H 82 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7966 (tp30) REVERT: L 96 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8020 (mp) outliers start: 18 outliers final: 10 residues processed: 56 average time/residue: 0.8610 time to fit residues: 50.6940 Evaluate side-chains 51 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.0870 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.160726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.125701 restraints weight = 4194.067| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.79 r_work: 0.3210 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4027 Z= 0.114 Angle : 0.519 5.077 5492 Z= 0.276 Chirality : 0.047 0.278 613 Planarity : 0.004 0.040 699 Dihedral : 4.934 30.553 601 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.96 % Allowed : 18.20 % Favored : 76.83 % 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: 0.22 (0.38), residues: 487 helix: 1.61 (0.93), residues: 23 sheet: 1.08 (0.37), residues: 200 loop : -0.76 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 107 HIS 0.003 0.001 HIS A 66 PHE 0.013 0.001 PHE A 175 TYR 0.011 0.001 TYR A 279 ARG 0.001 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00855 ( 3) link_NAG-ASN : angle 2.61083 ( 9) hydrogen bonds : bond 0.03189 ( 141) hydrogen bonds : angle 4.89614 ( 372) SS BOND : bond 0.00526 ( 5) SS BOND : angle 1.28023 ( 10) covalent geometry : bond 0.00264 ( 4019) covalent geometry : angle 0.50587 ( 5473) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 37 time to evaluate : 0.400 Fit side-chains REVERT: A 154 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: H 32 ASN cc_start: 0.9072 (m110) cc_final: 0.8542 (m-40) REVERT: H 38 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7740 (ttm170) REVERT: H 51 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7696 (tp) REVERT: H 82 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: H 100 ASN cc_start: 0.8501 (p0) cc_final: 0.8300 (p0) REVERT: L 96 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7981 (mp) outliers start: 21 outliers final: 12 residues processed: 52 average time/residue: 0.9092 time to fit residues: 49.6537 Evaluate side-chains 55 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.160160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125733 restraints weight = 4288.295| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.01 r_work: 0.3189 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4027 Z= 0.158 Angle : 0.589 9.514 5492 Z= 0.313 Chirality : 0.047 0.165 613 Planarity : 0.004 0.040 699 Dihedral : 5.207 33.740 601 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 6.62 % Allowed : 17.02 % Favored : 76.36 % 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: 0.13 (0.37), residues: 487 helix: 1.53 (0.94), residues: 23 sheet: 1.00 (0.37), residues: 200 loop : -0.80 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 107 HIS 0.004 0.001 HIS A 66 PHE 0.020 0.002 PHE A 175 TYR 0.013 0.002 TYR A 279 ARG 0.002 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 3) link_NAG-ASN : angle 2.13605 ( 9) hydrogen bonds : bond 0.03749 ( 141) hydrogen bonds : angle 4.98717 ( 372) SS BOND : bond 0.00572 ( 5) SS BOND : angle 3.07967 ( 10) covalent geometry : bond 0.00383 ( 4019) covalent geometry : angle 0.56814 ( 5473) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 41 time to evaluate : 0.416 Fit side-chains REVERT: A 129 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8481 (ttmm) REVERT: A 154 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8324 (mt-10) REVERT: H 32 ASN cc_start: 0.9118 (m110) cc_final: 0.8625 (m-40) REVERT: H 38 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7746 (ttm170) REVERT: H 51 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7779 (tp) REVERT: H 82 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8027 (tp30) REVERT: H 100 ASN cc_start: 0.8494 (p0) cc_final: 0.8261 (p0) REVERT: L 96 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8094 (mp) outliers start: 28 outliers final: 16 residues processed: 62 average time/residue: 0.7995 time to fit residues: 52.2027 Evaluate side-chains 57 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.0050 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.0020 chunk 32 optimal weight: 0.0470 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.162932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.127825 restraints weight = 4198.190| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.80 r_work: 0.3241 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4027 Z= 0.100 Angle : 0.501 6.013 5492 Z= 0.268 Chirality : 0.045 0.153 613 Planarity : 0.004 0.040 699 Dihedral : 4.730 27.073 601 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.67 % Allowed : 17.97 % Favored : 76.36 % 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: 0.26 (0.38), residues: 487 helix: 1.70 (0.94), residues: 23 sheet: 1.12 (0.38), residues: 199 loop : -0.73 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 107 HIS 0.002 0.001 HIS A 66 PHE 0.013 0.001 PHE A 133 TYR 0.010 0.001 TYR A 279 ARG 0.001 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 3) link_NAG-ASN : angle 2.22115 ( 9) hydrogen bonds : bond 0.02969 ( 141) hydrogen bonds : angle 4.84335 ( 372) SS BOND : bond 0.00379 ( 5) SS BOND : angle 1.95682 ( 10) covalent geometry : bond 0.00229 ( 4019) covalent geometry : angle 0.48613 ( 5473) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 39 time to evaluate : 0.524 Fit side-chains REVERT: A 129 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8439 (ttmm) REVERT: A 154 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: A 249 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8345 (tp) REVERT: H 32 ASN cc_start: 0.9059 (m110) cc_final: 0.8533 (m-40) REVERT: H 38 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7726 (ttm170) REVERT: H 82 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: H 100 ASN cc_start: 0.8445 (p0) cc_final: 0.8103 (p0) REVERT: L 96 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7968 (mp) outliers start: 24 outliers final: 15 residues processed: 56 average time/residue: 0.8119 time to fit residues: 48.0521 Evaluate side-chains 62 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.157840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123935 restraints weight = 4232.010| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.02 r_work: 0.3164 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4027 Z= 0.213 Angle : 0.650 7.017 5492 Z= 0.343 Chirality : 0.049 0.180 613 Planarity : 0.004 0.039 699 Dihedral : 5.514 38.013 601 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.91 % Allowed : 18.91 % Favored : 75.18 % 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: 0.02 (0.37), residues: 487 helix: 1.32 (0.92), residues: 23 sheet: 0.97 (0.37), residues: 201 loop : -0.90 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 107 HIS 0.005 0.002 HIS A 66 PHE 0.027 0.002 PHE A 175 TYR 0.016 0.002 TYR A 279 ARG 0.002 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 3) link_NAG-ASN : angle 2.32222 ( 9) hydrogen bonds : bond 0.04485 ( 141) hydrogen bonds : angle 5.15871 ( 372) SS BOND : bond 0.00719 ( 5) SS BOND : angle 1.93541 ( 10) covalent geometry : bond 0.00526 ( 4019) covalent geometry : angle 0.63910 ( 5473) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 36 time to evaluate : 0.413 Fit side-chains REVERT: A 129 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8532 (ttmm) REVERT: A 132 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8118 (mt-10) REVERT: A 154 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8486 (mt-10) REVERT: H 38 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7751 (ttm170) REVERT: H 82 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8007 (tp30) REVERT: H 100 ASN cc_start: 0.8494 (p0) cc_final: 0.8271 (p0) REVERT: L 96 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8173 (mp) outliers start: 25 outliers final: 16 residues processed: 57 average time/residue: 0.8551 time to fit residues: 51.1740 Evaluate side-chains 53 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 32 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.159432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.125491 restraints weight = 4175.616| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.04 r_work: 0.3184 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4027 Z= 0.158 Angle : 0.582 6.071 5492 Z= 0.309 Chirality : 0.047 0.169 613 Planarity : 0.004 0.040 699 Dihedral : 5.219 34.313 601 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.67 % Allowed : 18.68 % Favored : 75.65 % 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: 0.00 (0.37), residues: 487 helix: 1.41 (0.93), residues: 23 sheet: 0.96 (0.38), residues: 199 loop : -0.92 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 107 HIS 0.004 0.001 HIS A 66 PHE 0.020 0.002 PHE A 175 TYR 0.014 0.002 TYR A 279 ARG 0.001 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 3) link_NAG-ASN : angle 2.40750 ( 9) hydrogen bonds : bond 0.03862 ( 141) hydrogen bonds : angle 5.07464 ( 372) SS BOND : bond 0.00556 ( 5) SS BOND : angle 1.54574 ( 10) covalent geometry : bond 0.00383 ( 4019) covalent geometry : angle 0.57118 ( 5473) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 36 time to evaluate : 0.394 Fit side-chains REVERT: A 129 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8487 (ttmm) REVERT: A 132 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8084 (mt-10) REVERT: A 154 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: H 38 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7716 (ttm170) REVERT: H 82 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: H 100 ASN cc_start: 0.8535 (p0) cc_final: 0.8311 (p0) REVERT: L 96 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8068 (mp) outliers start: 24 outliers final: 17 residues processed: 56 average time/residue: 0.9137 time to fit residues: 53.6591 Evaluate side-chains 56 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 34 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.159986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125627 restraints weight = 4206.869| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.87 r_work: 0.3199 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4027 Z= 0.143 Angle : 0.563 5.968 5492 Z= 0.299 Chirality : 0.047 0.166 613 Planarity : 0.004 0.041 699 Dihedral : 5.037 34.045 601 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.67 % Allowed : 18.91 % Favored : 75.41 % 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: 0.03 (0.37), residues: 487 helix: 1.31 (0.93), residues: 23 sheet: 0.98 (0.38), residues: 199 loop : -0.89 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 107 HIS 0.003 0.001 HIS A 66 PHE 0.018 0.002 PHE A 175 TYR 0.012 0.001 TYR A 279 ARG 0.001 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 3) link_NAG-ASN : angle 2.43590 ( 9) hydrogen bonds : bond 0.03691 ( 141) hydrogen bonds : angle 4.99769 ( 372) SS BOND : bond 0.00542 ( 5) SS BOND : angle 1.44489 ( 10) covalent geometry : bond 0.00345 ( 4019) covalent geometry : angle 0.55217 ( 5473) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 36 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8442 (ttmm) REVERT: A 132 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8156 (mt-10) REVERT: A 154 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8356 (mt-10) REVERT: A 249 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8396 (tp) REVERT: H 38 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7734 (ttm170) REVERT: H 82 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: H 100 ASN cc_start: 0.8528 (p0) cc_final: 0.8119 (p0) REVERT: L 96 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8026 (mp) outliers start: 24 outliers final: 15 residues processed: 55 average time/residue: 0.9019 time to fit residues: 52.0009 Evaluate side-chains 55 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 34 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.158569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124168 restraints weight = 4232.490| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.87 r_work: 0.3185 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 4027 Z= 0.202 Angle : 0.682 11.475 5492 Z= 0.357 Chirality : 0.049 0.176 613 Planarity : 0.004 0.040 699 Dihedral : 5.543 36.249 601 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.67 % Allowed : 18.68 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.13 (0.37), residues: 487 helix: 1.03 (0.93), residues: 23 sheet: 0.97 (0.38), residues: 196 loop : -1.06 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 107 HIS 0.004 0.001 HIS A 66 PHE 0.025 0.002 PHE A 175 TYR 0.015 0.002 TYR A 279 ARG 0.002 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 3) link_NAG-ASN : angle 2.90672 ( 9) hydrogen bonds : bond 0.04258 ( 141) hydrogen bonds : angle 5.11179 ( 372) SS BOND : bond 0.00714 ( 5) SS BOND : angle 3.71812 ( 10) covalent geometry : bond 0.00499 ( 4019) covalent geometry : angle 0.65363 ( 5473) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 34 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 154 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8436 (mt-10) REVERT: A 249 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8445 (tp) REVERT: H 38 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7751 (ttm170) REVERT: H 100 ASN cc_start: 0.8548 (p0) cc_final: 0.8130 (p0) REVERT: L 96 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8124 (mp) outliers start: 24 outliers final: 17 residues processed: 55 average time/residue: 0.8706 time to fit residues: 50.3339 Evaluate side-chains 53 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 32 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 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 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.159196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.124520 restraints weight = 4180.233| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.98 r_work: 0.3148 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 4027 Z= 0.140 Angle : 0.596 9.668 5492 Z= 0.316 Chirality : 0.047 0.166 613 Planarity : 0.004 0.041 699 Dihedral : 5.178 33.151 601 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.96 % Allowed : 19.62 % Favored : 75.41 % 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: -0.05 (0.37), residues: 487 helix: 1.29 (0.94), residues: 23 sheet: 0.99 (0.38), residues: 197 loop : -1.00 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 107 HIS 0.003 0.001 HIS A 66 PHE 0.016 0.002 PHE A 175 TYR 0.012 0.001 TYR A 279 ARG 0.001 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 3) link_NAG-ASN : angle 2.62849 ( 9) hydrogen bonds : bond 0.03541 ( 141) hydrogen bonds : angle 4.98226 ( 372) SS BOND : bond 0.00466 ( 5) SS BOND : angle 3.12366 ( 10) covalent geometry : bond 0.00337 ( 4019) covalent geometry : angle 0.57173 ( 5473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3587.51 seconds wall clock time: 62 minutes 29.85 seconds (3749.85 seconds total)