Starting phenix.real_space_refine on Thu Oct 22 21:59:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lv5_63413/10_2026/9lv5_63413.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lv5_63413/10_2026/9lv5_63413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lv5_63413/10_2026/9lv5_63413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lv5_63413/10_2026/9lv5_63413.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lv5_63413/10_2026/9lv5_63413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lv5_63413/10_2026/9lv5_63413.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 6 Type Number sf(0) Gaussians P 125 5.49 5 Mg 1 5.21 5 S 13 5.16 5 C 3422 2.51 5 N 1083 2.21 5 O 1498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6142 Number of models: 1 Model: "" Number of chains: 4 Chain: "P" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "R" Number of atoms: 2578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2578 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 9, 'rna3p_pur': 51, 'rna3p_pyr': 50} Link IDs: {'rna2p': 20, 'rna3p': 100} Chain breaks: 4 Chain: "A" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3481 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 411} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.34, per 1000 atoms: 0.22 Number of scatterers: 6142 At special positions: 0 Unit cell: (67.23, 98.82, 133.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 13 16.00 P 125 15.00 Mg 1 11.99 O 1498 8.00 N 1083 7.00 C 3422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 222.7 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 54.6% alpha, 12.5% beta 45 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 76 through 101 removed outlier: 3.628A pdb=" N GLY A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 237 through 246 removed outlier: 4.139A pdb=" N MET A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.612A pdb=" N ARG A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 279 through 292 removed outlier: 4.268A pdb=" N ALA A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.514A pdb=" N THR A 303 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 368 removed outlier: 3.687A pdb=" N LEU A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 385 Processing helix chain 'A' and resid 391 through 404 Processing helix chain 'A' and resid 405 through 413 removed outlier: 4.040A pdb=" N LYS A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 425 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 74 Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 267 removed outlier: 3.748A pdb=" N ILE A 309 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 323 187 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 977 1.33 - 1.45: 2295 1.45 - 1.57: 2985 1.57 - 1.69: 244 1.69 - 1.81: 22 Bond restraints: 6523 Sorted by residual: bond pdb=" C3' DT P 4 " pdb=" O3' DT P 4 " ideal model delta sigma weight residual 1.435 1.407 0.028 1.30e-02 5.92e+03 4.52e+00 bond pdb=" C4' DT P 4 " pdb=" C3' DT P 4 " ideal model delta sigma weight residual 1.529 1.508 0.021 1.00e-02 1.00e+04 4.50e+00 bond pdb=" C4' DT P 2 " pdb=" C3' DT P 2 " ideal model delta sigma weight residual 1.529 1.510 0.019 1.00e-02 1.00e+04 3.61e+00 bond pdb=" C4' DA P 3 " pdb=" C3' DA P 3 " ideal model delta sigma weight residual 1.529 1.511 0.018 1.00e-02 1.00e+04 3.16e+00 bond pdb=" C3' DT P 2 " pdb=" O3' DT P 2 " ideal model delta sigma weight residual 1.435 1.413 0.022 1.30e-02 5.92e+03 2.89e+00 ... (remaining 6518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 8909 1.88 - 3.75: 459 3.75 - 5.63: 12 5.63 - 7.51: 3 7.51 - 9.39: 1 Bond angle restraints: 9384 Sorted by residual: angle pdb=" O4' DT P 4 " pdb=" C4' DT P 4 " pdb=" C3' DT P 4 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" O5' U R 173 " pdb=" C5' U R 173 " pdb=" C4' U R 173 " ideal model delta sigma weight residual 109.40 112.62 -3.22 8.00e-01 1.56e+00 1.62e+01 angle pdb=" N3 DT P 4 " pdb=" C4 DT P 4 " pdb=" O4 DT P 4 " ideal model delta sigma weight residual 119.90 122.29 -2.39 6.00e-01 2.78e+00 1.59e+01 angle pdb=" N3 DT P 2 " pdb=" C4 DT P 2 " pdb=" O4 DT P 2 " ideal model delta sigma weight residual 119.90 122.21 -2.31 6.00e-01 2.78e+00 1.49e+01 angle pdb=" O4 DT P 4 " pdb=" C4 DT P 4 " pdb=" C5 DT P 4 " ideal model delta sigma weight residual 124.90 122.23 2.67 7.00e-01 2.04e+00 1.45e+01 ... (remaining 9379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.10: 3506 24.10 - 48.21: 378 48.21 - 72.31: 192 72.31 - 96.41: 24 96.41 - 120.51: 1 Dihedral angle restraints: 4101 sinusoidal: 2838 harmonic: 1263 Sorted by residual: dihedral pdb=" O4' U R 243 " pdb=" C1' U R 243 " pdb=" N1 U R 243 " pdb=" C2 U R 243 " ideal model delta sinusoidal sigma weight residual -128.00 -58.56 -69.44 1 1.70e+01 3.46e-03 2.16e+01 dihedral pdb=" O4' G R 261 " pdb=" C1' G R 261 " pdb=" N9 G R 261 " pdb=" C4 G R 261 " ideal model delta sinusoidal sigma weight residual 68.00 14.55 53.45 1 1.70e+01 3.46e-03 1.34e+01 dihedral pdb=" CA LEU A 294 " pdb=" C LEU A 294 " pdb=" N LYS A 295 " pdb=" CA LYS A 295 " ideal model delta harmonic sigma weight residual 180.00 162.80 17.20 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 4098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 763 0.040 - 0.079: 191 0.079 - 0.119: 67 0.119 - 0.159: 106 0.159 - 0.198: 4 Chirality restraints: 1131 Sorted by residual: chirality pdb=" CA TYR A 86 " pdb=" N TYR A 86 " pdb=" C TYR A 86 " pdb=" CB TYR A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" C3' A R 210 " pdb=" C4' A R 210 " pdb=" O3' A R 210 " pdb=" C2' A R 210 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CG LEU A 23 " pdb=" CB LEU A 23 " pdb=" CD1 LEU A 23 " pdb=" CD2 LEU A 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 1128 not shown) Planarity restraints: 731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 42 " -0.065 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A 43 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U R 258 " 0.021 2.00e-02 2.50e+03 1.09e-02 2.68e+00 pdb=" N1 U R 258 " -0.023 2.00e-02 2.50e+03 pdb=" C2 U R 258 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U R 258 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U R 258 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U R 258 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U R 258 " 0.007 2.00e-02 2.50e+03 pdb=" C5 U R 258 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U R 258 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 6 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 7 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 7 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 7 " -0.023 5.00e-02 4.00e+02 ... (remaining 728 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 39 2.54 - 3.13: 4369 3.13 - 3.72: 10678 3.72 - 4.31: 14424 4.31 - 4.90: 21220 Nonbonded interactions: 50730 Sorted by model distance: nonbonded pdb=" OD2 ASP A 140 " pdb="MG MG A 501 " model vdw 1.947 2.170 nonbonded pdb=" OD1 ASP A 250 " pdb=" OH TYR A 264 " model vdw 2.067 3.040 nonbonded pdb=" O2' U R 204 " pdb=" OP1 G R 206 " model vdw 2.183 3.040 nonbonded pdb=" OG1 THR A 208 " pdb=" OD1 ASP A 211 " model vdw 2.198 3.040 nonbonded pdb=" OP1 A R 198 " pdb=" NZ LYS A 373 " model vdw 2.221 3.120 ... (remaining 50725 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: 0.900 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.100 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 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 : 0.004 0.039 6523 Z= 0.262 Angle : 0.749 9.386 9384 Z= 0.578 Chirality : 0.055 0.198 1131 Planarity : 0.006 0.098 731 Dihedral : 20.956 120.515 3287 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 21.18 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.40), residues: 423 helix: 1.43 (0.36), residues: 213 sheet: 0.97 (0.68), residues: 49 loop : -0.33 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 383 TYR 0.020 0.002 TYR A 201 PHE 0.023 0.003 PHE A 328 TRP 0.011 0.002 TRP A 157 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.26 ( 6523) covalent geometry : angle 0.74868 / 0.58 ( 9384) hydrogen bonds : bond 0.12516 / 12.84 ( 295) hydrogen bonds : angle 5.04995 / 6.08 ( 715) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6750 (ttm) cc_final: 0.6338 (ttm) REVERT: A 253 MET cc_start: 0.6638 (mmt) cc_final: 0.6423 (mmt) REVERT: A 367 ASN cc_start: 0.7519 (t0) cc_final: 0.7287 (t0) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1042 time to fit residues: 10.1325 Evaluate side-chains 76 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [54, 24, 48, 26, 2, 16, 32, 31, 25, 50, 53] chunk 54 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.0870 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.196756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.164653 restraints weight = 9358.542| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.24 r_work: 0.3914 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6523 Z= 0.122 Angle : 0.493 8.376 9384 Z= 0.280 Chirality : 0.036 0.276 1131 Planarity : 0.005 0.069 731 Dihedral : 21.041 121.930 2400 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.61 % Allowed : 19.84 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.40), residues: 423 helix: 1.44 (0.36), residues: 215 sheet: 1.38 (0.70), residues: 49 loop : -0.10 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 390 TYR 0.008 0.001 TYR A 180 PHE 0.012 0.001 PHE A 171 TRP 0.004 0.001 TRP A 157 HIS 0.002 0.001 HIS A 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 6523) covalent geometry : angle 0.49268 / 0.28 ( 9384) hydrogen bonds : bond 0.05528 / 6.36 ( 295) hydrogen bonds : angle 4.14067 / 5.01 ( 715) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6840 (ttm) cc_final: 0.6473 (ttm) REVERT: A 253 MET cc_start: 0.7345 (mmt) cc_final: 0.7071 (mmt) REVERT: A 346 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6976 (mpp80) REVERT: A 367 ASN cc_start: 0.7730 (t0) cc_final: 0.7513 (t0) outliers start: 6 outliers final: 2 residues processed: 75 average time/residue: 0.0992 time to fit residues: 9.4146 Evaluate side-chains 73 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [21, 5, 6, 46, 48, 50, 8, 17, 15, 42, 47] chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN A 102 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.192989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.160623 restraints weight = 9158.271| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.28 r_work: 0.3883 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6523 Z= 0.204 Angle : 0.550 7.255 9384 Z= 0.309 Chirality : 0.040 0.272 1131 Planarity : 0.005 0.059 731 Dihedral : 20.991 121.732 2400 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.22 % Allowed : 20.11 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.40), residues: 423 helix: 1.13 (0.35), residues: 214 sheet: 1.49 (0.73), residues: 49 loop : -0.29 (0.47), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 390 TYR 0.013 0.002 TYR A 180 PHE 0.027 0.003 PHE A 328 TRP 0.008 0.002 TRP A 157 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 ( 6523) covalent geometry : angle 0.55016 / 0.31 ( 9384) hydrogen bonds : bond 0.06035 / 6.84 ( 295) hydrogen bonds : angle 4.07521 / 5.00 ( 715) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6956 (mpp80) outliers start: 12 outliers final: 6 residues processed: 80 average time/residue: 0.1029 time to fit residues: 10.3172 Evaluate side-chains 77 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [17, 22, 54, 21, 15, 37, 26, 18, 41, 20, 39] chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN A 106 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.194523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.162043 restraints weight = 9207.219| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.34 r_work: 0.3906 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6523 Z= 0.132 Angle : 0.476 7.408 9384 Z= 0.270 Chirality : 0.035 0.273 1131 Planarity : 0.005 0.058 731 Dihedral : 20.907 123.178 2400 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.68 % Allowed : 20.91 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.40), residues: 423 helix: 1.27 (0.36), residues: 214 sheet: 1.86 (0.73), residues: 47 loop : -0.29 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 383 TYR 0.014 0.001 TYR A 86 PHE 0.012 0.002 PHE A 328 TRP 0.002 0.001 TRP A 157 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 6523) covalent geometry : angle 0.47584 / 0.27 ( 9384) hydrogen bonds : bond 0.05152 / 5.84 ( 295) hydrogen bonds : angle 3.94584 / 4.83 ( 715) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 TYR cc_start: 0.6726 (t80) cc_final: 0.6510 (t80) REVERT: A 246 MET cc_start: 0.6198 (ptp) cc_final: 0.5984 (ptp) REVERT: A 253 MET cc_start: 0.7507 (mmt) cc_final: 0.7252 (mmt) REVERT: A 346 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6984 (mpp80) outliers start: 10 outliers final: 5 residues processed: 76 average time/residue: 0.0996 time to fit residues: 9.5618 Evaluate side-chains 79 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [20, 37, 40, 18, 42, 49, 13, 54, 36, 44, 51] chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 18 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.192940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.160287 restraints weight = 9389.278| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.32 r_work: 0.3879 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6523 Z= 0.176 Angle : 0.506 7.373 9384 Z= 0.285 Chirality : 0.037 0.274 1131 Planarity : 0.004 0.049 731 Dihedral : 20.901 123.319 2400 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.02 % Allowed : 19.84 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.40), residues: 423 helix: 1.14 (0.36), residues: 214 sheet: 1.82 (0.73), residues: 47 loop : -0.24 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 383 TYR 0.014 0.002 TYR A 86 PHE 0.022 0.002 PHE A 328 TRP 0.006 0.001 TRP A 157 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 ( 6523) covalent geometry : angle 0.50604 / 0.28 ( 9384) hydrogen bonds : bond 0.05483 / 6.22 ( 295) hydrogen bonds : angle 3.94542 / 4.82 ( 715) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7521 (mmt) cc_final: 0.7233 (mmt) REVERT: A 311 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7446 (ttpt) REVERT: A 346 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6952 (mpp80) outliers start: 15 outliers final: 9 residues processed: 85 average time/residue: 0.0981 time to fit residues: 10.5258 Evaluate side-chains 82 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [33, 44, 2, 1, 6, 47, 54, 50, 26, 9, 13] chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.192249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.159575 restraints weight = 9206.781| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.31 r_work: 0.3863 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6523 Z= 0.179 Angle : 0.514 8.233 9384 Z= 0.289 Chirality : 0.038 0.277 1131 Planarity : 0.004 0.047 731 Dihedral : 20.921 123.726 2400 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.49 % Allowed : 20.91 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.40), residues: 423 helix: 1.05 (0.36), residues: 214 sheet: 1.42 (0.74), residues: 49 loop : -0.23 (0.47), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 383 TYR 0.017 0.002 TYR A 86 PHE 0.021 0.003 PHE A 328 TRP 0.007 0.001 TRP A 157 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 ( 6523) covalent geometry : angle 0.51355 / 0.29 ( 9384) hydrogen bonds : bond 0.05523 / 6.24 ( 295) hydrogen bonds : angle 3.97733 / 4.83 ( 715) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7505 (mmt) cc_final: 0.7229 (mmt) REVERT: A 346 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6950 (mpp80) outliers start: 13 outliers final: 9 residues processed: 82 average time/residue: 0.0913 time to fit residues: 9.5424 Evaluate side-chains 82 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [31, 51, 23, 5, 47, 26, 13, 54, 52, 19, 15] chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 23 optimal weight: 0.4980 chunk 5 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.194038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.161842 restraints weight = 9261.869| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.30 r_work: 0.3893 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6523 Z= 0.121 Angle : 0.467 8.257 9384 Z= 0.264 Chirality : 0.035 0.272 1131 Planarity : 0.004 0.045 731 Dihedral : 20.843 125.607 2400 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.49 % Allowed : 22.25 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.41), residues: 423 helix: 1.32 (0.36), residues: 214 sheet: 1.93 (0.74), residues: 47 loop : -0.09 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 390 TYR 0.019 0.002 TYR A 174 PHE 0.012 0.001 PHE A 144 TRP 0.003 0.001 TRP A 157 HIS 0.002 0.001 HIS A 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 6523) covalent geometry : angle 0.46730 / 0.26 ( 9384) hydrogen bonds : bond 0.04919 / 5.55 ( 295) hydrogen bonds : angle 3.84389 / 4.67 ( 715) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7482 (mmt) cc_final: 0.7265 (mmt) REVERT: A 311 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7478 (ttpt) REVERT: A 346 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6993 (mpp80) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.0991 time to fit residues: 9.5309 Evaluate side-chains 81 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [15, 22, 28, 20, 43, 38, 32, 39, 12, 14, 2] chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.192587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.159903 restraints weight = 9277.041| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.29 r_work: 0.3867 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6523 Z= 0.169 Angle : 0.511 9.235 9384 Z= 0.285 Chirality : 0.037 0.275 1131 Planarity : 0.004 0.044 731 Dihedral : 20.841 125.052 2400 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.75 % Allowed : 21.98 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.41), residues: 423 helix: 1.16 (0.36), residues: 214 sheet: 1.84 (0.74), residues: 47 loop : -0.11 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 365 TYR 0.019 0.002 TYR A 174 PHE 0.020 0.002 PHE A 328 TRP 0.008 0.001 TRP A 157 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 6523) covalent geometry : angle 0.51063 / 0.29 ( 9384) hydrogen bonds : bond 0.05313 / 5.98 ( 295) hydrogen bonds : angle 3.89244 / 4.74 ( 715) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7496 (mmt) cc_final: 0.7235 (mmt) REVERT: A 346 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6986 (mpp80) outliers start: 14 outliers final: 9 residues processed: 78 average time/residue: 0.0977 time to fit residues: 9.5933 Evaluate side-chains 79 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [22, 9, 39, 30, 54, 52, 16, 29, 4, 48, 14] chunk 22 optimal weight: 0.1980 chunk 9 optimal weight: 30.0000 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 40.0000 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.193669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.161329 restraints weight = 9321.716| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.30 r_work: 0.3891 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6523 Z= 0.135 Angle : 0.493 9.507 9384 Z= 0.276 Chirality : 0.035 0.272 1131 Planarity : 0.004 0.043 731 Dihedral : 20.822 125.894 2400 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.02 % Allowed : 21.98 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.41), residues: 423 helix: 1.25 (0.36), residues: 214 sheet: 1.79 (0.74), residues: 47 loop : -0.11 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 365 TYR 0.020 0.002 TYR A 174 PHE 0.025 0.002 PHE A 110 TRP 0.005 0.001 TRP A 157 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 6523) covalent geometry : angle 0.49343 / 0.28 ( 9384) hydrogen bonds : bond 0.04978 / 5.61 ( 295) hydrogen bonds : angle 3.88326 / 4.73 ( 715) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 CYS cc_start: 0.6150 (m) cc_final: 0.5612 (m) REVERT: A 253 MET cc_start: 0.7502 (mmt) cc_final: 0.7260 (mmt) REVERT: A 346 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6994 (mpp80) outliers start: 15 outliers final: 11 residues processed: 79 average time/residue: 0.1052 time to fit residues: 10.2479 Evaluate side-chains 82 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [54, 18, 8, 26, 30, 38, 42, 48, 52, 45, 27] chunk 54 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.193378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.160878 restraints weight = 9283.331| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.30 r_work: 0.3878 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6523 Z= 0.154 Angle : 0.515 9.653 9384 Z= 0.285 Chirality : 0.036 0.272 1131 Planarity : 0.004 0.043 731 Dihedral : 20.809 125.999 2400 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.49 % Allowed : 21.98 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.41), residues: 423 helix: 1.18 (0.36), residues: 214 sheet: 1.74 (0.74), residues: 47 loop : -0.14 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 365 TYR 0.019 0.002 TYR A 174 PHE 0.017 0.002 PHE A 110 TRP 0.008 0.001 TRP A 157 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 6523) covalent geometry : angle 0.51471 / 0.29 ( 9384) hydrogen bonds : bond 0.05138 / 5.78 ( 295) hydrogen bonds : angle 3.89739 / 4.77 ( 715) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8217 (mtmm) cc_final: 0.8014 (ptpp) REVERT: A 134 CYS cc_start: 0.6160 (m) cc_final: 0.5683 (m) REVERT: A 175 LYS cc_start: 0.7597 (mtmp) cc_final: 0.7346 (pttm) REVERT: A 253 MET cc_start: 0.7460 (mmt) cc_final: 0.7224 (mmt) REVERT: A 346 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6968 (mpp80) outliers start: 13 outliers final: 10 residues processed: 76 average time/residue: 0.1027 time to fit residues: 9.7481 Evaluate side-chains 80 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [29, 41, 14, 48, 24, 16, 51, 33, 31, 0, 26] chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.189479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.157295 restraints weight = 9274.910| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.17 r_work: 0.3901 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6523 Z= 0.132 Angle : 0.497 9.951 9384 Z= 0.277 Chirality : 0.035 0.271 1131 Planarity : 0.004 0.043 731 Dihedral : 20.785 126.569 2400 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.49 % Allowed : 22.25 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.41), residues: 423 helix: 1.28 (0.36), residues: 214 sheet: 1.78 (0.73), residues: 47 loop : -0.12 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 365 TYR 0.018 0.002 TYR A 174 PHE 0.013 0.002 PHE A 328 TRP 0.005 0.001 TRP A 157 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 6523) covalent geometry : angle 0.49661 / 0.28 ( 9384) hydrogen bonds : bond 0.04899 / 5.52 ( 295) hydrogen bonds : angle 3.87024 / 4.74 ( 715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1561.76 seconds wall clock time: 27 minutes 25.58 seconds (1645.58 seconds total)