Starting phenix.real_space_refine on Thu Nov 14 16:41:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0j_45086/11_2024/9c0j_45086.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0j_45086/11_2024/9c0j_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0j_45086/11_2024/9c0j_45086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0j_45086/11_2024/9c0j_45086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0j_45086/11_2024/9c0j_45086.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0j_45086/11_2024/9c0j_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-5513/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: 5.15, per 1000 atoms: 0.73 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: 2.30 Conformation dependent library (CDL) restraints added in 464.5 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: 3.63 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: 2.69 Time building geometry restraints manager: 2.51 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: 0.010 Normalize map: mean=0, sd=1: 0.600 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: 0.060 Set scattering table: 0.060 Process input model: 24.380 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.190 ------------------------------------------------------------------------------- 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 : 0.660 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: 0.4031 time to fit residues: 28.6266 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 : 0.556 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 : 0.501 Fit side-chains REVERT: A 198 ASN cc_start: 0.8607 (t0) cc_final: 0.8336 (t0) REVERT: A 205 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8038 (mtpp) REVERT: A 259 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7286 (mt-10) REVERT: A 329 ASP cc_start: 0.8447 (p0) cc_final: 0.8237 (p0) REVERT: A 352 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.7863 (mtt90) outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.3427 time to fit residues: 21.0985 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 : 0.553 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.4980 chunk 43 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7493 Z= 0.265 Angle : 0.627 6.654 10897 Z= 0.324 Chirality : 0.038 0.241 1324 Planarity : 0.005 0.035 771 Dihedral : 22.778 148.867 2989 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.16 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: 1.04 (0.40), residues: 423 helix: 1.21 (0.35), residues: 212 sheet: 1.07 (0.62), residues: 64 loop : -0.12 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 157 HIS 0.003 0.001 HIS A 263 PHE 0.009 0.002 PHE A 328 TYR 0.016 0.002 TYR A 245 ARG 0.003 0.001 ARG A 383 *********************** 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 : 0.551 Fit side-chains REVERT: A 352 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.7878 (mtt90) outliers start: 5 outliers final: 4 residues processed: 46 average time/residue: 0.3212 time to fit residues: 18.2293 Evaluate side-chains 45 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7493 Z= 0.269 Angle : 0.619 6.780 10897 Z= 0.318 Chirality : 0.038 0.235 1324 Planarity : 0.005 0.036 771 Dihedral : 22.752 149.375 2989 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.68 % Allowed : 8.31 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.40), residues: 423 helix: 1.33 (0.36), residues: 212 sheet: 1.00 (0.63), residues: 64 loop : -0.23 (0.48), 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 170 PHE 0.011 0.002 PHE A 328 TYR 0.016 0.002 TYR A 245 ARG 0.003 0.001 ARG A 352 *********************** 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 53 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.556 Fit side-chains REVERT: A 119 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: A 352 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.7873 (mtt90) outliers start: 10 outliers final: 8 residues processed: 51 average time/residue: 0.2833 time to fit residues: 18.0977 Evaluate side-chains 50 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 41 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 0.0870 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7493 Z= 0.275 Angle : 0.621 6.678 10897 Z= 0.319 Chirality : 0.038 0.232 1324 Planarity : 0.005 0.037 771 Dihedral : 22.686 149.296 2989 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 0.99 (0.40), residues: 423 helix: 1.33 (0.36), residues: 211 sheet: 1.01 (0.63), residues: 64 loop : -0.40 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 157 HIS 0.004 0.001 HIS A 170 PHE 0.010 0.002 PHE A 328 TYR 0.015 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 55 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.516 Fit side-chains REVERT: A 352 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.7868 (mtt90) outliers start: 11 outliers final: 10 residues processed: 50 average time/residue: 0.3002 time to fit residues: 18.6140 Evaluate side-chains 50 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL 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 304 GLU 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 13 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 0.0270 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 6 optimal weight: 0.0670 chunk 31 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 0.003 0.039 7493 Z= 0.199 Angle : 0.587 6.586 10897 Z= 0.303 Chirality : 0.035 0.231 1324 Planarity : 0.004 0.038 771 Dihedral : 22.680 148.947 2989 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.22 % Allowed : 9.12 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.40), residues: 423 helix: 1.51 (0.36), residues: 211 sheet: 1.06 (0.63), residues: 64 loop : -0.43 (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 0.009 0.001 PHE A 47 TYR 0.015 0.001 TYR A 245 ARG 0.002 0.000 ARG A 260 *********************** 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 50 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.613 Fit side-chains REVERT: A 119 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: A 352 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.7882 (mtt90) outliers start: 12 outliers final: 9 residues processed: 45 average time/residue: 0.3141 time to fit residues: 17.6555 Evaluate side-chains 48 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 346 ARG 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 31 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7493 Z= 0.243 Angle : 0.599 6.696 10897 Z= 0.308 Chirality : 0.036 0.232 1324 Planarity : 0.004 0.038 771 Dihedral : 22.660 148.843 2989 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.95 % Allowed : 9.38 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.40), residues: 423 helix: 1.51 (0.36), residues: 211 sheet: 1.08 (0.63), residues: 64 loop : -0.51 (0.48), residues: 148 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 0.002 0.000 ARG A 123 *********************** 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: 11 poor density : 41 time to evaluate : 0.559 Fit side-chains REVERT: A 119 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: A 352 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.7871 (mtt90) outliers start: 11 outliers final: 9 residues processed: 48 average time/residue: 0.2942 time to fit residues: 17.6952 Evaluate side-chains 50 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 304 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 48 optimal weight: 30.0000 chunk 51 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 7493 Z= 0.420 Angle : 0.716 7.829 10897 Z= 0.362 Chirality : 0.042 0.237 1324 Planarity : 0.005 0.039 771 Dihedral : 22.843 149.707 2989 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.22 % Allowed : 10.19 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.58 (0.40), residues: 423 helix: 1.11 (0.35), residues: 211 sheet: 0.57 (0.63), residues: 66 loop : -0.67 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 157 HIS 0.003 0.001 HIS A 170 PHE 0.013 0.002 PHE A 328 TYR 0.016 0.002 TYR A 245 ARG 0.004 0.001 ARG A 123 *********************** 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 55 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.456 Fit side-chains REVERT: A 119 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: A 352 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.7856 (mtt90) outliers start: 12 outliers final: 8 residues processed: 51 average time/residue: 0.3190 time to fit residues: 19.9839 Evaluate side-chains 50 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 48 optimal weight: 30.0000 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7493 Z= 0.177 Angle : 0.581 6.460 10897 Z= 0.300 Chirality : 0.035 0.230 1324 Planarity : 0.004 0.038 771 Dihedral : 22.724 146.994 2989 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 1.03 (0.41), residues: 423 helix: 1.54 (0.36), residues: 211 sheet: 0.83 (0.62), residues: 67 loop : -0.61 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 157 HIS 0.003 0.001 HIS A 16 PHE 0.008 0.001 PHE A 47 TYR 0.011 0.001 TYR A 86 ARG 0.003 0.000 ARG A 254 *********************** 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 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.576 Fit side-chains REVERT: A 119 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: A 352 ARG cc_start: 0.8448 (ttm-80) cc_final: 0.7932 (mtt180) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.2698 time to fit residues: 15.4788 Evaluate side-chains 47 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 30.0000 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7493 Z= 0.229 Angle : 0.594 6.535 10897 Z= 0.305 Chirality : 0.036 0.230 1324 Planarity : 0.004 0.040 771 Dihedral : 22.690 148.518 2989 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.88 % Allowed : 10.99 % 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: 1.05 (0.40), residues: 423 helix: 1.57 (0.36), residues: 211 sheet: 0.78 (0.62), residues: 67 loop : -0.61 (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 0.009 0.001 PHE A 47 TYR 0.013 0.002 TYR A 245 ARG 0.002 0.000 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 47 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.571 Fit side-chains REVERT: A 119 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: A 352 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.7875 (mtt90) outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.3104 time to fit residues: 17.4792 Evaluate side-chains 47 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.166817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.113877 restraints weight = 6973.261| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 0.78 r_work: 0.2696 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7493 Z= 0.242 Angle : 0.598 6.692 10897 Z= 0.306 Chirality : 0.036 0.229 1324 Planarity : 0.005 0.042 771 Dihedral : 22.683 148.469 2989 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.41 % Allowed : 10.46 % 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: 1.04 (0.40), residues: 423 helix: 1.57 (0.36), residues: 211 sheet: 0.79 (0.62), residues: 67 loop : -0.61 (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 0.009 0.001 PHE A 47 TYR 0.014 0.002 TYR A 14 ARG 0.002 0.000 ARG A 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1415.64 seconds wall clock time: 30 minutes 27.62 seconds (1827.62 seconds total)