Starting phenix.real_space_refine on Tue Jan 14 14:46:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0j_45086/01_2025/9c0j_45086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0j_45086/01_2025/9c0j_45086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c0j_45086/01_2025/9c0j_45086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0j_45086/01_2025/9c0j_45086.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0j_45086/01_2025/9c0j_45086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0j_45086/01_2025/9c0j_45086.cif" } resolution = 3.17 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= 0.004 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 167 5.49 5 Mg 1 5.21 5 S 13 5.16 5 C 3809 2.51 5 N 1240 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7010 Number of models: 1 Model: "" Number of chains: 5 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: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "R" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3313 Classifications: {'RNA': 155} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 10, 'rna3p_pur': 67, 'rna3p_pyr': 61} Link IDs: {'rna2p': 26, 'rna3p': 128} Chain breaks: 4 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.97, per 1000 atoms: 0.71 Number of scatterers: 7010 At special positions: 0 Unit cell: (131.716, 110.5, 79.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 13 16.00 P 167 15.00 Mg 1 11.99 O 1779 8.00 N 1240 7.00 C 3809 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: 2.33 Conformation dependent library (CDL) restraints added in 603.5 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: 18 helices and 3 sheets defined 53.4% alpha, 13.6% beta 58 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.603A pdb=" N LYS A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.630A pdb=" N ILE A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 38 " --> pdb=" O GLU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 101 removed outlier: 4.132A pdb=" N GLY A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 101 " --> pdb=" O LEU A 97 " (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: 3.731A pdb=" N MET A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.728A pdb=" N ARG A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.772A pdb=" N ALA A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 336 through 368 removed outlier: 3.865A pdb=" N LEU A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.827A 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 403 Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.937A 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 63 through 74 removed outlier: 3.780A pdb=" N ARG A 70 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 49 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A 44 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 267 removed outlier: 3.645A pdb=" N CYS A 134 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 314 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 323 181 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 816 1.32 - 1.44: 2984 1.44 - 1.56: 3337 1.56 - 1.68: 334 1.68 - 1.81: 22 Bond restraints: 7493 Sorted by residual: bond pdb=" C LYS A 205 " pdb=" O LYS A 205 " ideal model delta sigma weight residual 1.234 1.193 0.041 1.28e-02 6.10e+03 1.04e+01 bond pdb=" CB ASP A 329 " pdb=" CG ASP A 329 " ideal model delta sigma weight residual 1.516 1.582 -0.066 2.50e-02 1.60e+03 6.99e+00 bond pdb=" C1' DT P 8 " pdb=" N1 DT P 8 " ideal model delta sigma weight residual 1.490 1.568 -0.078 3.00e-02 1.11e+03 6.77e+00 bond pdb=" C1' DT P 5 " pdb=" N1 DT P 5 " ideal model delta sigma weight residual 1.490 1.567 -0.077 3.00e-02 1.11e+03 6.51e+00 bond pdb=" N CYS A 207 " pdb=" CA CYS A 207 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.23e-02 6.61e+03 4.24e+00 ... (remaining 7488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 10341 2.04 - 4.08: 449 4.08 - 6.13: 81 6.13 - 8.17: 18 8.17 - 10.21: 8 Bond angle restraints: 10897 Sorted by residual: angle pdb=" C LYS A 311 " pdb=" N ASP A 312 " pdb=" CA ASP A 312 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" O3' A R 210 " pdb=" C3' A R 210 " pdb=" C2' A R 210 " ideal model delta sigma weight residual 113.70 121.37 -7.67 1.50e+00 4.44e-01 2.62e+01 angle pdb=" CA ARG A 390 " pdb=" CB ARG A 390 " pdb=" CG ARG A 390 " ideal model delta sigma weight residual 114.10 123.91 -9.81 2.00e+00 2.50e-01 2.41e+01 angle pdb=" N LYS A 205 " pdb=" CA LYS A 205 " pdb=" C LYS A 205 " ideal model delta sigma weight residual 110.14 102.94 7.20 1.55e+00 4.16e-01 2.16e+01 angle pdb=" CA ASP A 329 " pdb=" CB ASP A 329 " pdb=" CG ASP A 329 " ideal model delta sigma weight residual 112.60 117.06 -4.46 1.00e+00 1.00e+00 1.98e+01 ... (remaining 10892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.66: 4126 28.66 - 57.32: 345 57.32 - 85.98: 202 85.98 - 114.63: 7 114.63 - 143.29: 6 Dihedral angle restraints: 4686 sinusoidal: 3423 harmonic: 1263 Sorted by residual: dihedral pdb=" O4' U R 134 " pdb=" C1' U R 134 " pdb=" N1 U R 134 " pdb=" C2 U R 134 " ideal model delta sinusoidal sigma weight residual -160.00 -67.13 -92.87 1 1.50e+01 4.44e-03 4.48e+01 dihedral pdb=" C2 TTP A 502 " pdb=" C1' TTP A 502 " pdb=" N1 TTP A 502 " pdb=" O4' TTP A 502 " ideal model delta sinusoidal sigma weight residual 301.68 158.39 143.29 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" O2G TTP A 502 " pdb=" O3B TTP A 502 " pdb=" PG TTP A 502 " pdb=" PB TTP A 502 " ideal model delta sinusoidal sigma weight residual 180.00 49.01 130.99 1 2.00e+01 2.50e-03 3.97e+01 ... (remaining 4683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1162 0.073 - 0.145: 138 0.145 - 0.218: 19 0.218 - 0.291: 4 0.291 - 0.363: 1 Chirality restraints: 1324 Sorted by residual: 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 -2.11 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" C1' U R 173 " pdb=" O4' U R 173 " pdb=" C2' U R 173 " pdb=" N1 U R 173 " both_signs ideal model delta sigma weight residual False 2.47 2.18 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C1' U R 224 " pdb=" O4' U R 224 " pdb=" C2' U R 224 " pdb=" N1 U R 224 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1321 not shown) Planarity restraints: 771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 254 " -0.226 9.50e-02 1.11e+02 1.02e-01 7.97e+00 pdb=" NE ARG A 254 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 254 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 254 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 254 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 302 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C LYS A 302 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS A 302 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 303 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 204 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C ARG A 204 " 0.046 2.00e-02 2.50e+03 pdb=" O ARG A 204 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 205 " -0.016 2.00e-02 2.50e+03 ... (remaining 768 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.71: 374 2.71 - 3.32: 6416 3.32 - 3.92: 15484 3.92 - 4.53: 20134 4.53 - 5.14: 27208 Nonbonded interactions: 69616 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O1B TTP A 502 " model vdw 2.099 2.170 nonbonded pdb=" OD2 ASP A 269 " pdb="MG MG A 501 " model vdw 2.119 2.170 nonbonded pdb=" O LEU A 141 " pdb="MG MG A 501 " model vdw 2.307 2.170 nonbonded pdb=" O TYR A 381 " pdb=" OG SER A 385 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR A 86 " pdb=" OD2 ASP A 169 " model vdw 2.385 3.040 ... (remaining 69611 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: 0.760 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 22.240 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 : 0.005 0.078 7493 Z= 0.307 Angle : 1.022 10.208 10897 Z= 0.539 Chirality : 0.051 0.363 1324 Planarity : 0.009 0.102 771 Dihedral : 22.014 143.293 3872 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.80 % Allowed : 4.29 % Favored : 94.91 % 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: -0.50 (0.36), residues: 423 helix: -0.83 (0.29), residues: 209 sheet: 1.28 (0.67), residues: 55 loop : 0.07 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 8 HIS 0.006 0.002 HIS A 81 PHE 0.021 0.003 PHE A 212 TYR 0.021 0.003 TYR A 89 ARG 0.022 0.002 ARG A 254 *********************** 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 59 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.568 Fit side-chains REVERT: A 198 ASN cc_start: 0.8565 (t0) cc_final: 0.8305 (t0) REVERT: A 205 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8058 (mtpp) REVERT: A 246 MET cc_start: 0.8827 (mmm) cc_final: 0.8615 (mmt) REVERT: A 259 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7290 (mt-10) REVERT: A 319 MET cc_start: 0.8333 (mtm) cc_final: 0.7992 (mtp) REVERT: A 329 ASP cc_start: 0.8330 (p0) cc_final: 0.8072 (p0) outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.3805 time to fit residues: 26.5750 Evaluate side-chains 43 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 30.0000 chunk 43 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.167466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.118003 restraints weight = 6997.786| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 0.69 r_work: 0.2815 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7493 Z= 0.164 Angle : 0.570 6.382 10897 Z= 0.302 Chirality : 0.036 0.235 1324 Planarity : 0.004 0.034 771 Dihedral : 22.863 146.612 2990 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.07 % Allowed : 5.63 % Favored : 93.30 % 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: 1.11 (0.39), residues: 423 helix: 0.96 (0.34), residues: 212 sheet: 1.66 (0.68), residues: 53 loop : 0.27 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 157 HIS 0.003 0.001 HIS A 81 PHE 0.011 0.001 PHE A 52 TYR 0.012 0.001 TYR A 245 ARG 0.005 0.001 ARG A 254 *********************** 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 53 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.579 Fit side-chains REVERT: A 198 ASN cc_start: 0.8611 (t0) cc_final: 0.8334 (t0) REVERT: A 205 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8004 (mtpp) REVERT: A 259 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7627 (mt-10) REVERT: A 329 ASP cc_start: 0.8531 (p0) cc_final: 0.8320 (p0) REVERT: A 352 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.7911 (mtt90) outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.3615 time to fit residues: 22.2809 Evaluate side-chains 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 39 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.163622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.111555 restraints weight = 7113.656| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 0.78 r_work: 0.2705 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7493 Z= 0.251 Angle : 0.617 6.691 10897 Z= 0.319 Chirality : 0.038 0.241 1324 Planarity : 0.004 0.035 771 Dihedral : 22.761 148.423 2989 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.34 % Allowed : 8.04 % Favored : 90.62 % 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: 1.09 (0.40), residues: 423 helix: 1.26 (0.35), residues: 212 sheet: 1.07 (0.62), residues: 64 loop : -0.11 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 157 HIS 0.003 0.001 HIS A 263 PHE 0.009 0.002 PHE A 328 TYR 0.015 0.002 TYR A 245 ARG 0.003 0.001 ARG A 254 *********************** 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 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.500 Fit side-chains REVERT: A 352 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.7963 (mtt90) outliers start: 5 outliers final: 5 residues processed: 46 average time/residue: 0.3113 time to fit residues: 17.7879 Evaluate side-chains 47 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.163293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.111445 restraints weight = 7126.888| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 0.73 r_work: 0.2721 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7493 Z= 0.244 Angle : 0.606 6.666 10897 Z= 0.313 Chirality : 0.037 0.239 1324 Planarity : 0.005 0.035 771 Dihedral : 22.738 148.676 2989 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.95 % Allowed : 8.85 % Favored : 88.20 % 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: 1.14 (0.40), residues: 423 helix: 1.41 (0.36), residues: 212 sheet: 1.08 (0.64), residues: 64 loop : -0.25 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 157 HIS 0.003 0.001 HIS A 81 PHE 0.011 0.002 PHE A 47 TYR 0.014 0.002 TYR A 245 ARG 0.004 0.001 ARG A 123 *********************** 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 56 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.558 Fit side-chains REVERT: A 119 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: A 352 ARG cc_start: 0.8507 (ttm-80) cc_final: 0.7973 (mtt90) outliers start: 11 outliers final: 8 residues processed: 52 average time/residue: 0.3181 time to fit residues: 20.2968 Evaluate side-chains 51 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 47 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.161755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.110138 restraints weight = 7079.574| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 0.74 r_work: 0.2672 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7493 Z= 0.311 Angle : 0.644 6.765 10897 Z= 0.329 Chirality : 0.039 0.233 1324 Planarity : 0.005 0.037 771 Dihedral : 22.743 149.421 2989 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.22 % Allowed : 8.31 % Favored : 88.47 % 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: 0.90 (0.40), residues: 423 helix: 1.28 (0.36), residues: 211 sheet: 1.04 (0.64), residues: 64 loop : -0.52 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 157 HIS 0.003 0.001 HIS A 170 PHE 0.010 0.002 PHE A 328 TYR 0.014 0.002 TYR A 245 ARG 0.003 0.001 ARG A 123 *********************** 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 56 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.550 Fit side-chains REVERT: A 119 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: A 164 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7855 (mp0) REVERT: A 352 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.7955 (mtt90) outliers start: 12 outliers final: 9 residues processed: 52 average time/residue: 0.2886 time to fit residues: 18.6721 Evaluate side-chains 52 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 6.9990 chunk 48 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 2 optimal weight: 0.0980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.163043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.111709 restraints weight = 7082.192| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 0.70 r_work: 0.2705 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7493 Z= 0.194 Angle : 0.598 6.557 10897 Z= 0.309 Chirality : 0.036 0.232 1324 Planarity : 0.004 0.038 771 Dihedral : 22.733 149.238 2989 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.95 % Allowed : 9.65 % Favored : 87.40 % 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: 1.08 (0.40), residues: 423 helix: 1.47 (0.36), residues: 211 sheet: 1.15 (0.64), residues: 64 loop : -0.53 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 157 HIS 0.003 0.001 HIS A 170 PHE 0.010 0.001 PHE A 52 TYR 0.014 0.001 TYR A 245 ARG 0.002 0.000 ARG A 254 *********************** 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 54 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.565 Fit side-chains REVERT: A 119 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: A 164 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7831 (mp0) REVERT: A 352 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.7966 (mtt90) outliers start: 11 outliers final: 10 residues processed: 50 average time/residue: 0.3224 time to fit residues: 19.6836 Evaluate side-chains 53 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.163883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.113455 restraints weight = 7063.795| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 0.74 r_work: 0.2731 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7493 Z= 0.178 Angle : 0.581 6.488 10897 Z= 0.300 Chirality : 0.035 0.229 1324 Planarity : 0.004 0.036 771 Dihedral : 22.706 148.629 2989 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.14 % Allowed : 10.46 % Favored : 87.40 % 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: 1.18 (0.41), residues: 423 helix: 1.60 (0.36), residues: 211 sheet: 1.18 (0.64), residues: 64 loop : -0.55 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 157 HIS 0.003 0.001 HIS A 263 PHE 0.011 0.001 PHE A 52 TYR 0.012 0.001 TYR A 245 ARG 0.003 0.001 ARG A 383 *********************** 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 52 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.529 Fit side-chains REVERT: A 53 LYS cc_start: 0.7252 (pttt) cc_final: 0.6684 (mmtm) REVERT: A 119 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: A 352 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.8008 (mtt180) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.3135 time to fit residues: 19.2467 Evaluate side-chains 50 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 47 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.163611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.112653 restraints weight = 7086.138| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 0.73 r_work: 0.2716 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7493 Z= 0.214 Angle : 0.586 6.673 10897 Z= 0.301 Chirality : 0.036 0.230 1324 Planarity : 0.004 0.036 771 Dihedral : 22.663 148.562 2989 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.22 % Allowed : 9.65 % Favored : 87.13 % 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: 1.16 (0.40), residues: 423 helix: 1.61 (0.36), residues: 211 sheet: 1.12 (0.64), residues: 64 loop : -0.59 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 157 HIS 0.003 0.001 HIS A 170 PHE 0.018 0.002 PHE A 52 TYR 0.012 0.001 TYR A 245 ARG 0.003 0.000 ARG A 306 *********************** 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 56 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.517 Fit side-chains REVERT: A 53 LYS cc_start: 0.7277 (pttt) cc_final: 0.6708 (mmtm) REVERT: A 352 ARG cc_start: 0.8521 (ttm-80) cc_final: 0.7973 (mtt90) outliers start: 12 outliers final: 8 residues processed: 50 average time/residue: 0.3210 time to fit residues: 19.6126 Evaluate side-chains 51 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 6 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.161083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.109188 restraints weight = 7159.664| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 0.73 r_work: 0.2653 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7493 Z= 0.354 Angle : 0.665 6.799 10897 Z= 0.338 Chirality : 0.039 0.236 1324 Planarity : 0.005 0.038 771 Dihedral : 22.768 149.544 2989 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.95 % Allowed : 10.19 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.40), residues: 423 helix: 1.32 (0.36), residues: 211 sheet: 0.66 (0.63), residues: 66 loop : -0.63 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 157 HIS 0.004 0.001 HIS A 170 PHE 0.012 0.002 PHE A 328 TYR 0.014 0.002 TYR A 245 ARG 0.003 0.001 ARG A 123 *********************** 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 53 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.580 Fit side-chains REVERT: A 119 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: A 352 ARG cc_start: 0.8584 (ttm-80) cc_final: 0.7994 (mtt90) outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 0.3058 time to fit residues: 18.9217 Evaluate side-chains 51 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 15 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.163219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.111449 restraints weight = 7185.260| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 0.75 r_work: 0.2683 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7493 Z= 0.186 Angle : 0.599 6.596 10897 Z= 0.309 Chirality : 0.036 0.234 1324 Planarity : 0.004 0.039 771 Dihedral : 22.757 149.297 2989 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.14 % Allowed : 10.72 % Favored : 87.13 % 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: 1.02 (0.41), residues: 423 helix: 1.54 (0.36), residues: 211 sheet: 0.79 (0.64), residues: 66 loop : -0.61 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 157 HIS 0.002 0.001 HIS A 77 PHE 0.009 0.001 PHE A 47 TYR 0.013 0.002 TYR A 245 ARG 0.002 0.001 ARG A 346 ********************** 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 50 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.531 Fit side-chains REVERT: A 53 LYS cc_start: 0.7247 (pttt) cc_final: 0.6653 (mmtm) REVERT: A 119 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: A 352 ARG cc_start: 0.8530 (ttm-80) cc_final: 0.7978 (mtt90) outliers start: 8 outliers final: 7 residues processed: 48 average time/residue: 0.3310 time to fit residues: 19.5195 Evaluate side-chains 50 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.162697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.111005 restraints weight = 7069.255| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 0.76 r_work: 0.2698 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7493 Z= 0.243 Angle : 0.608 6.604 10897 Z= 0.312 Chirality : 0.036 0.232 1324 Planarity : 0.005 0.041 771 Dihedral : 22.717 148.882 2989 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.68 % Allowed : 10.19 % Favored : 87.13 % 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: 0.97 (0.40), residues: 423 helix: 1.48 (0.36), residues: 211 sheet: 0.86 (0.63), residues: 67 loop : -0.67 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 157 HIS 0.003 0.001 HIS A 170 PHE 0.010 0.002 PHE A 47 TYR 0.013 0.002 TYR A 245 ARG 0.003 0.000 ARG A 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.49 seconds wall clock time: 58 minutes 38.90 seconds (3518.90 seconds total)