Starting phenix.real_space_refine on Thu Nov 14 00:47:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tte_41605/11_2024/8tte_41605.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tte_41605/11_2024/8tte_41605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tte_41605/11_2024/8tte_41605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tte_41605/11_2024/8tte_41605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tte_41605/11_2024/8tte_41605.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tte_41605/11_2024/8tte_41605.cif" } resolution = 3.26 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= 0.001 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2015 2.51 5 N 454 2.21 5 O 504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2991 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2842 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 149 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 13} Time building chain proxies: 2.55, per 1000 atoms: 0.85 Number of scatterers: 2991 At special positions: 0 Unit cell: (55.704, 73.428, 75.116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 504 8.00 N 454 7.00 C 2015 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 456.8 milliseconds 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 694 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 1 sheets defined 88.8% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 21 removed outlier: 3.549A pdb=" N ILE A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.748A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 66 removed outlier: 3.576A pdb=" N LEU A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 67 through 86 removed outlier: 3.631A pdb=" N ALA A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 120 removed outlier: 3.705A pdb=" N LEU A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 121 through 125 removed outlier: 4.070A pdb=" N LYS A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 148 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 157 through 177 Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.994A pdb=" N LYS A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 199' Processing helix chain 'A' and resid 204 through 233 removed outlier: 4.006A pdb=" N SER A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 264 removed outlier: 5.726A pdb=" N ASP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 289 Processing helix chain 'A' and resid 291 through 308 removed outlier: 3.732A pdb=" N SER A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 removed outlier: 3.844A pdb=" N ALA A 312 " --> pdb=" O MET A 308 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 354 removed outlier: 3.804A pdb=" N ALA A 328 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Proline residue: A 344 - end of helix removed outlier: 3.736A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 382 Processing sheet with id=AA1, first strand: chain 'C' and resid 129 through 132 245 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 858 1.34 - 1.46: 650 1.46 - 1.58: 1530 1.58 - 1.70: 0 1.70 - 1.82: 35 Bond restraints: 3073 Sorted by residual: bond pdb=" CE1 HIS A 123 " pdb=" NE2 HIS A 123 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.71e+01 bond pdb=" N VAL A 365 " pdb=" CA VAL A 365 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.13e+00 bond pdb=" N VAL A 108 " pdb=" CA VAL A 108 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.20e-02 6.94e+03 7.98e+00 bond pdb=" N VAL A 302 " pdb=" CA VAL A 302 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.95e+00 bond pdb=" N ILE A 199 " pdb=" CA ILE A 199 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.24e-02 6.50e+03 7.89e+00 ... (remaining 3068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 3918 1.90 - 3.81: 223 3.81 - 5.71: 21 5.71 - 7.61: 2 7.61 - 9.51: 3 Bond angle restraints: 4167 Sorted by residual: angle pdb=" N LEU A 17 " pdb=" CA LEU A 17 " pdb=" C LEU A 17 " ideal model delta sigma weight residual 111.69 105.40 6.29 1.23e+00 6.61e-01 2.62e+01 angle pdb=" CB MET A 361 " pdb=" CG MET A 361 " pdb=" SD MET A 361 " ideal model delta sigma weight residual 112.70 122.21 -9.51 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CB MET A 263 " pdb=" CG MET A 263 " pdb=" SD MET A 263 " ideal model delta sigma weight residual 112.70 103.36 9.34 3.00e+00 1.11e-01 9.69e+00 angle pdb=" N MET A 157 " pdb=" CA MET A 157 " pdb=" C MET A 157 " ideal model delta sigma weight residual 109.81 116.65 -6.84 2.21e+00 2.05e-01 9.57e+00 angle pdb=" N PHE A 262 " pdb=" CA PHE A 262 " pdb=" CB PHE A 262 " ideal model delta sigma weight residual 110.30 114.90 -4.60 1.54e+00 4.22e-01 8.94e+00 ... (remaining 4162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 1476 16.16 - 32.32: 202 32.32 - 48.48: 59 48.48 - 64.64: 12 64.64 - 80.80: 2 Dihedral angle restraints: 1751 sinusoidal: 658 harmonic: 1093 Sorted by residual: dihedral pdb=" CA TRP C 131 " pdb=" C TRP C 131 " pdb=" N TYR C 132 " pdb=" CA TYR C 132 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ARG A 156 " pdb=" C ARG A 156 " pdb=" N MET A 157 " pdb=" CA MET A 157 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TYR A 235 " pdb=" C TYR A 235 " pdb=" N SER A 236 " pdb=" CA SER A 236 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 1748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 321 0.047 - 0.095: 100 0.095 - 0.142: 42 0.142 - 0.189: 12 0.189 - 0.237: 4 Chirality restraints: 479 Sorted by residual: chirality pdb=" CA LEU A 17 " pdb=" N LEU A 17 " pdb=" C LEU A 17 " pdb=" CB LEU A 17 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE A 12 " pdb=" N ILE A 12 " pdb=" C ILE A 12 " pdb=" CB ILE A 12 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE A 53 " pdb=" N ILE A 53 " pdb=" C ILE A 53 " pdb=" CB ILE A 53 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 476 not shown) Planarity restraints: 506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 262 " 0.021 2.00e-02 2.50e+03 2.30e-02 9.29e+00 pdb=" CG PHE A 262 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 262 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 262 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A 262 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 262 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 262 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 157 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.92e+00 pdb=" C MET A 157 " -0.052 2.00e-02 2.50e+03 pdb=" O MET A 157 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO A 158 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 233 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C VAL A 233 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL A 233 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN A 234 " 0.008 2.00e-02 2.50e+03 ... (remaining 503 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 891 2.82 - 3.34: 3284 3.34 - 3.86: 5129 3.86 - 4.38: 5547 4.38 - 4.90: 9715 Nonbonded interactions: 24566 Sorted by model distance: nonbonded pdb=" OG SER A 236 " pdb=" OD1 ASP A 239 " model vdw 2.301 3.040 nonbonded pdb=" NZ LYS A 68 " pdb=" O ILE A 177 " model vdw 2.365 3.120 nonbonded pdb=" OG1 THR A 36 " pdb=" OD1 ASP A 352 " model vdw 2.396 3.040 nonbonded pdb=" N SER A 38 " pdb=" OD2 ASP A 352 " model vdw 2.404 3.120 nonbonded pdb=" O LEU A 276 " pdb=" OG SER A 279 " model vdw 2.476 3.040 ... (remaining 24561 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: 0.920 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.170 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 : 0.006 0.041 3073 Z= 0.374 Angle : 0.915 9.513 4167 Z= 0.632 Chirality : 0.059 0.237 479 Planarity : 0.004 0.030 506 Dihedral : 16.553 80.796 1057 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.94 % Allowed : 28.53 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.55 (0.44), residues: 379 helix: 1.04 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -2.71 (0.73), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 PHE 0.053 0.002 PHE A 262 TYR 0.019 0.001 TYR A 278 ARG 0.002 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.379 Fit side-chains REVERT: A 156 ARG cc_start: 0.6732 (mtm180) cc_final: 0.5692 (mtp85) outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 0.1551 time to fit residues: 13.3550 Evaluate side-chains 66 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.0010 chunk 22 optimal weight: 0.0020 chunk 34 optimal weight: 0.0770 chunk 10 optimal weight: 0.5980 overall best weight: 0.2752 ------------------------------------------------------------------------------- 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: 0.7762 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3073 Z= 0.180 Angle : 0.646 6.943 4167 Z= 0.335 Chirality : 0.041 0.173 479 Planarity : 0.004 0.028 506 Dihedral : 4.554 19.139 407 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.08 % Allowed : 28.53 % Favored : 67.40 % 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: 1.87 (0.46), residues: 379 helix: 1.93 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.40 (0.85), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 201 HIS 0.004 0.001 HIS A 379 PHE 0.040 0.001 PHE A 262 TYR 0.018 0.001 TYR A 278 ARG 0.003 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.317 Fit side-chains REVERT: A 5 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7234 (tp) REVERT: A 235 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.7011 (m-10) REVERT: A 376 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7960 (tm-30) outliers start: 13 outliers final: 6 residues processed: 78 average time/residue: 0.1374 time to fit residues: 13.2593 Evaluate side-chains 73 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7821 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3073 Z= 0.229 Angle : 0.678 8.266 4167 Z= 0.346 Chirality : 0.041 0.164 479 Planarity : 0.004 0.025 506 Dihedral : 4.485 19.160 405 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.70 % Allowed : 28.53 % Favored : 66.77 % 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: 1.97 (0.46), residues: 379 helix: 1.97 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.23 (0.89), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 PHE 0.012 0.002 PHE A 16 TYR 0.014 0.001 TYR A 278 ARG 0.002 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.320 Fit side-chains REVERT: A 51 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7322 (tp40) REVERT: A 76 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8603 (mm) REVERT: A 150 MET cc_start: 0.7208 (pmm) cc_final: 0.6678 (pmm) REVERT: A 235 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.7027 (m-10) REVERT: A 352 ASP cc_start: 0.7930 (m-30) cc_final: 0.7729 (m-30) outliers start: 15 outliers final: 7 residues processed: 80 average time/residue: 0.1288 time to fit residues: 12.9029 Evaluate side-chains 76 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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: 0.7844 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3073 Z= 0.241 Angle : 0.690 6.888 4167 Z= 0.353 Chirality : 0.043 0.165 479 Planarity : 0.004 0.032 506 Dihedral : 4.506 19.197 405 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.64 % Allowed : 28.53 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.46), residues: 379 helix: 1.97 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -2.23 (0.86), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.007 0.001 HIS A 379 PHE 0.048 0.002 PHE A 262 TYR 0.013 0.001 TYR A 278 ARG 0.003 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.334 Fit side-chains REVERT: A 51 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7344 (tp40) REVERT: A 76 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8612 (mm) REVERT: A 150 MET cc_start: 0.7101 (pmm) cc_final: 0.6642 (pmm) REVERT: A 235 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.7345 (m-10) outliers start: 18 outliers final: 12 residues processed: 75 average time/residue: 0.1407 time to fit residues: 12.9809 Evaluate side-chains 78 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.0270 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.0670 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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: 0.7809 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3073 Z= 0.195 Angle : 0.661 6.831 4167 Z= 0.340 Chirality : 0.041 0.165 479 Planarity : 0.004 0.034 506 Dihedral : 4.453 19.676 405 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 6.58 % Allowed : 27.59 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.46), residues: 379 helix: 2.03 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -2.11 (0.88), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 PHE 0.012 0.001 PHE A 16 TYR 0.014 0.001 TYR A 278 ARG 0.005 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.325 Fit side-chains REVERT: A 51 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7412 (tp40) REVERT: A 61 LEU cc_start: 0.7965 (tt) cc_final: 0.6694 (mp) REVERT: A 76 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8586 (mm) REVERT: A 235 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7466 (m-10) outliers start: 21 outliers final: 12 residues processed: 84 average time/residue: 0.1315 time to fit residues: 13.9280 Evaluate side-chains 81 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7807 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3073 Z= 0.204 Angle : 0.687 9.497 4167 Z= 0.345 Chirality : 0.042 0.158 479 Planarity : 0.004 0.032 506 Dihedral : 4.400 18.758 405 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.64 % Allowed : 28.53 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.47), residues: 379 helix: 1.93 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.00 (0.93), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 PHE 0.054 0.002 PHE A 262 TYR 0.013 0.001 TYR A 278 ARG 0.004 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.289 Fit side-chains REVERT: A 51 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7328 (tp40) REVERT: A 61 LEU cc_start: 0.7928 (tt) cc_final: 0.6695 (mp) REVERT: A 76 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8576 (mm) REVERT: A 235 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7571 (m-10) outliers start: 18 outliers final: 12 residues processed: 74 average time/residue: 0.1349 time to fit residues: 12.4418 Evaluate side-chains 81 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7837 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3073 Z= 0.234 Angle : 0.697 8.385 4167 Z= 0.354 Chirality : 0.042 0.159 479 Planarity : 0.005 0.049 506 Dihedral : 4.454 17.888 405 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.64 % Allowed : 29.78 % Favored : 64.58 % 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: 1.83 (0.46), residues: 379 helix: 1.95 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -2.28 (0.87), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 201 HIS 0.006 0.001 HIS A 379 PHE 0.012 0.002 PHE A 16 TYR 0.012 0.001 TYR A 278 ARG 0.008 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.246 Fit side-chains REVERT: A 51 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7348 (tp40) REVERT: A 76 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8574 (mm) REVERT: A 235 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7661 (m-10) outliers start: 18 outliers final: 14 residues processed: 78 average time/residue: 0.1462 time to fit residues: 13.8725 Evaluate side-chains 82 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 0.0000 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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: 0.7827 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3073 Z= 0.218 Angle : 0.703 9.435 4167 Z= 0.352 Chirality : 0.042 0.157 479 Planarity : 0.005 0.048 506 Dihedral : 4.475 18.887 405 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.33 % Allowed : 31.35 % Favored : 63.32 % 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: 1.94 (0.47), residues: 379 helix: 1.94 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -2.12 (0.92), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 PHE 0.012 0.001 PHE A 159 TYR 0.012 0.001 TYR A 278 ARG 0.008 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.321 Fit side-chains REVERT: A 51 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7314 (tp40) REVERT: A 76 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8563 (mm) REVERT: A 235 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7660 (m-10) outliers start: 17 outliers final: 12 residues processed: 76 average time/residue: 0.1436 time to fit residues: 13.3733 Evaluate side-chains 81 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 0.0370 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.0270 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3073 Z= 0.191 Angle : 0.712 10.214 4167 Z= 0.356 Chirality : 0.042 0.161 479 Planarity : 0.004 0.040 506 Dihedral : 4.415 19.503 405 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.39 % Allowed : 31.03 % Favored : 64.58 % 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: 2.04 (0.47), residues: 379 helix: 2.03 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -2.17 (0.90), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 201 HIS 0.004 0.001 HIS A 379 PHE 0.012 0.001 PHE A 16 TYR 0.013 0.001 TYR A 278 ARG 0.006 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.322 Fit side-chains REVERT: A 51 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7281 (tp40) REVERT: A 76 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8520 (mm) REVERT: A 235 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7629 (m-10) outliers start: 14 outliers final: 10 residues processed: 75 average time/residue: 0.1540 time to fit residues: 14.1597 Evaluate side-chains 78 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3073 Z= 0.222 Angle : 0.730 10.106 4167 Z= 0.367 Chirality : 0.043 0.165 479 Planarity : 0.005 0.050 506 Dihedral : 4.479 19.907 405 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.08 % Allowed : 32.29 % Favored : 63.64 % 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: 1.96 (0.47), residues: 379 helix: 1.98 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -2.25 (0.90), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 PHE 0.013 0.002 PHE A 159 TYR 0.011 0.001 TYR A 278 ARG 0.008 0.001 ARG A 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.319 Fit side-chains REVERT: A 76 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8535 (mm) outliers start: 13 outliers final: 10 residues processed: 75 average time/residue: 0.1301 time to fit residues: 12.0958 Evaluate side-chains 77 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.171412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.151703 restraints weight = 3922.075| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.89 r_work: 0.3602 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3073 Z= 0.224 Angle : 0.733 9.750 4167 Z= 0.369 Chirality : 0.043 0.162 479 Planarity : 0.005 0.053 506 Dihedral : 4.498 19.072 405 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.08 % Allowed : 32.60 % Favored : 63.32 % 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: 1.89 (0.47), residues: 379 helix: 1.93 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.27 (0.89), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.005 0.001 HIS A 379 PHE 0.015 0.001 PHE A 149 TYR 0.021 0.001 TYR A 235 ARG 0.008 0.001 ARG A 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1111.23 seconds wall clock time: 20 minutes 45.32 seconds (1245.32 seconds total)