Starting phenix.real_space_refine on Thu Jul 18 17:22:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4n_42974/07_2024/8v4n_42974.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4n_42974/07_2024/8v4n_42974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4n_42974/07_2024/8v4n_42974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4n_42974/07_2024/8v4n_42974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4n_42974/07_2024/8v4n_42974.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4n_42974/07_2024/8v4n_42974.cif" } resolution = 2.43 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= 0.005 sd= 0.075 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 9 5.16 5 C 1303 2.51 5 N 373 2.21 5 O 382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2067 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2067 Classifications: {'peptide': 263} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Time building chain proxies: 2.82, per 1000 atoms: 1.36 Number of scatterers: 2067 At special positions: 0 Unit cell: (93.636, 65.892, 84.099, 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 9 16.00 O 382 8.00 N 373 7.00 C 1303 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 - 3.50 Amino acid : False - 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: 0.55 Conformation dependent library (CDL) restraints added in 452.4 milliseconds 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 482 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 3 sheets defined 36.5% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.518A pdb=" N ASN A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 132 Processing helix chain 'A' and resid 159 through 174 Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 7.069A pdb=" N ALA A 240 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG A 268 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N SER A 242 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N LEU A 266 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASP A 244 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ALA A 264 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 149 removed outlier: 3.980A pdb=" N GLY A 215 " --> pdb=" O TYR A 181 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 261 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: 0.41 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 710 1.34 - 1.46: 420 1.46 - 1.58: 964 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 2110 Sorted by residual: bond pdb=" N LEU A 278 " pdb=" CA LEU A 278 " ideal model delta sigma weight residual 1.462 1.486 -0.024 1.44e-02 4.82e+03 2.79e+00 bond pdb=" N GLU A 279 " pdb=" CA GLU A 279 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.90e-02 2.77e+03 1.92e+00 bond pdb=" C GLU A 279 " pdb=" O GLU A 279 " ideal model delta sigma weight residual 1.231 1.249 -0.018 2.00e-02 2.50e+03 8.01e-01 bond pdb=" C VAL A 150 " pdb=" O VAL A 150 " ideal model delta sigma weight residual 1.232 1.240 -0.008 8.90e-03 1.26e+04 7.68e-01 bond pdb=" CB PRO A 258 " pdb=" CG PRO A 258 " ideal model delta sigma weight residual 1.492 1.533 -0.041 5.00e-02 4.00e+02 6.66e-01 ... (remaining 2105 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.39: 63 106.39 - 113.29: 1126 113.29 - 120.18: 730 120.18 - 127.08: 915 127.08 - 133.97: 26 Bond angle restraints: 2860 Sorted by residual: angle pdb=" CA LEU A 278 " pdb=" C LEU A 278 " pdb=" O LEU A 278 " ideal model delta sigma weight residual 122.51 118.24 4.27 1.34e+00 5.57e-01 1.01e+01 angle pdb=" CA GLU A 279 " pdb=" C GLU A 279 " pdb=" O GLU A 279 " ideal model delta sigma weight residual 120.80 117.26 3.54 1.70e+00 3.46e-01 4.33e+00 angle pdb=" C GLU A 198 " pdb=" N HIS A 199 " pdb=" CA HIS A 199 " ideal model delta sigma weight residual 122.46 125.10 -2.64 1.41e+00 5.03e-01 3.51e+00 angle pdb=" N HIS A 201 " pdb=" CA HIS A 201 " pdb=" CB HIS A 201 " ideal model delta sigma weight residual 112.78 110.18 2.60 1.53e+00 4.27e-01 2.88e+00 angle pdb=" O LEU A 278 " pdb=" C LEU A 278 " pdb=" N GLU A 279 " ideal model delta sigma weight residual 122.83 124.92 -2.09 1.31e+00 5.83e-01 2.54e+00 ... (remaining 2855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 1137 16.40 - 32.80: 89 32.80 - 49.20: 24 49.20 - 65.61: 1 65.61 - 82.01: 7 Dihedral angle restraints: 1258 sinusoidal: 505 harmonic: 753 Sorted by residual: dihedral pdb=" CA HIS A 200 " pdb=" C HIS A 200 " pdb=" N HIS A 201 " pdb=" CA HIS A 201 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA HIS A 199 " pdb=" C HIS A 199 " pdb=" N HIS A 200 " pdb=" CA HIS A 200 " ideal model delta harmonic sigma weight residual 180.00 162.81 17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CG ARG A 103 " pdb=" CD ARG A 103 " pdb=" NE ARG A 103 " pdb=" CZ ARG A 103 " ideal model delta sinusoidal sigma weight residual -90.00 -134.50 44.50 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 1255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 198 0.029 - 0.059: 72 0.059 - 0.088: 18 0.088 - 0.117: 19 0.117 - 0.147: 8 Chirality restraints: 315 Sorted by residual: chirality pdb=" CA LEU A 278 " pdb=" N LEU A 278 " pdb=" C LEU A 278 " pdb=" CB LEU A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL A 246 " pdb=" N VAL A 246 " pdb=" C VAL A 246 " pdb=" CB VAL A 246 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 312 not shown) Planarity restraints: 376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 277 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.44e+00 pdb=" C THR A 277 " 0.032 2.00e-02 2.50e+03 pdb=" O THR A 277 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 278 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 257 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 258 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 186 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 187 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " -0.016 5.00e-02 4.00e+02 ... (remaining 373 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 412 2.79 - 3.32: 1733 3.32 - 3.84: 3189 3.84 - 4.37: 3604 4.37 - 4.90: 6338 Nonbonded interactions: 15276 Sorted by model distance: nonbonded pdb=" NH1 ARG A 19 " pdb=" O LEU A 109 " model vdw 2.260 2.520 nonbonded pdb=" N GLY A 159 " pdb=" OE2 GLU A 204 " model vdw 2.333 2.520 nonbonded pdb=" OD1 ASN A 10 " pdb=" NE1 TRP A 17 " model vdw 2.442 2.520 nonbonded pdb=" N GLU A 15 " pdb=" OE1 GLU A 15 " model vdw 2.588 2.520 nonbonded pdb=" O LEU A 278 " pdb=" C GLU A 279 " model vdw 2.623 3.270 ... (remaining 15271 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.090 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.610 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 2110 Z= 0.144 Angle : 0.494 5.020 2860 Z= 0.280 Chirality : 0.043 0.147 315 Planarity : 0.004 0.030 376 Dihedral : 14.214 82.006 776 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.93 % Allowed : 0.47 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.52), residues: 259 helix: 2.70 (0.56), residues: 87 sheet: -0.34 (0.70), residues: 57 loop : -0.70 (0.51), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 17 HIS 0.006 0.001 HIS A 201 PHE 0.011 0.001 PHE A 92 TYR 0.004 0.001 TYR A 190 ARG 0.001 0.000 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.237 Fit side-chains REVERT: A 74 MET cc_start: 0.7655 (mtm) cc_final: 0.7407 (pp-130) REVERT: A 145 ASN cc_start: 0.7392 (m110) cc_final: 0.7191 (m-40) REVERT: A 173 ASN cc_start: 0.8258 (t0) cc_final: 0.7988 (t0) outliers start: 2 outliers final: 0 residues processed: 51 average time/residue: 1.5009 time to fit residues: 77.6553 Evaluate side-chains 41 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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: 0.8578 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2110 Z= 0.281 Angle : 0.644 7.704 2860 Z= 0.342 Chirality : 0.049 0.162 315 Planarity : 0.005 0.034 376 Dihedral : 4.764 21.558 292 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.80 % Allowed : 11.68 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.63 (0.51), residues: 259 helix: 2.50 (0.56), residues: 86 sheet: -0.30 (0.70), residues: 56 loop : -0.80 (0.50), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 96 HIS 0.007 0.002 HIS A 199 PHE 0.019 0.002 PHE A 259 TYR 0.010 0.002 TYR A 131 ARG 0.003 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.236 Fit side-chains REVERT: A 25 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8236 (tp) REVERT: A 57 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7023 (mp10) REVERT: A 74 MET cc_start: 0.7789 (mtm) cc_final: 0.7472 (pp-130) REVERT: A 173 ASN cc_start: 0.8386 (t0) cc_final: 0.7982 (t0) outliers start: 6 outliers final: 2 residues processed: 43 average time/residue: 1.6303 time to fit residues: 71.0922 Evaluate side-chains 44 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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: 0.8555 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2110 Z= 0.196 Angle : 0.548 7.711 2860 Z= 0.292 Chirality : 0.045 0.133 315 Planarity : 0.004 0.034 376 Dihedral : 4.441 17.835 292 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.74 % Allowed : 14.49 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.61 (0.51), residues: 259 helix: 2.62 (0.57), residues: 87 sheet: -0.53 (0.68), residues: 58 loop : -0.84 (0.49), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 96 HIS 0.006 0.001 HIS A 199 PHE 0.015 0.002 PHE A 259 TYR 0.007 0.001 TYR A 131 ARG 0.002 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.239 Fit side-chains REVERT: A 57 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.6912 (mp10) REVERT: A 74 MET cc_start: 0.7789 (mtm) cc_final: 0.7467 (pp-130) REVERT: A 173 ASN cc_start: 0.8290 (t0) cc_final: 0.7936 (t0) outliers start: 8 outliers final: 3 residues processed: 40 average time/residue: 1.8586 time to fit residues: 75.3765 Evaluate side-chains 42 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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: 0.8597 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2110 Z= 0.287 Angle : 0.635 8.211 2860 Z= 0.340 Chirality : 0.049 0.146 315 Planarity : 0.005 0.037 376 Dihedral : 4.732 15.564 292 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.27 % Allowed : 14.95 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.36 (0.50), residues: 259 helix: 2.31 (0.57), residues: 87 sheet: -0.63 (0.67), residues: 58 loop : -0.91 (0.48), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 96 HIS 0.006 0.001 HIS A 7 PHE 0.019 0.002 PHE A 259 TYR 0.009 0.002 TYR A 131 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.247 Fit side-chains REVERT: A 25 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8200 (tp) REVERT: A 57 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.6907 (mp10) REVERT: A 74 MET cc_start: 0.7782 (mtm) cc_final: 0.7477 (pp-130) REVERT: A 173 ASN cc_start: 0.8344 (t0) cc_final: 0.7987 (t0) REVERT: A 199 HIS cc_start: 0.5940 (p-80) cc_final: 0.4297 (t70) outliers start: 7 outliers final: 3 residues processed: 42 average time/residue: 1.6724 time to fit residues: 71.2798 Evaluate side-chains 45 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.8581 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2110 Z= 0.238 Angle : 0.589 8.350 2860 Z= 0.315 Chirality : 0.046 0.135 315 Planarity : 0.005 0.038 376 Dihedral : 4.552 15.337 292 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.21 % Allowed : 14.95 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.42 (0.50), residues: 259 helix: 2.46 (0.57), residues: 87 sheet: -0.51 (0.67), residues: 56 loop : -1.03 (0.47), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 96 HIS 0.005 0.001 HIS A 199 PHE 0.017 0.002 PHE A 259 TYR 0.008 0.001 TYR A 131 ARG 0.002 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.234 Fit side-chains REVERT: A 25 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8217 (tp) REVERT: A 57 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.6899 (mp10) REVERT: A 74 MET cc_start: 0.7770 (mtm) cc_final: 0.7480 (pp-130) REVERT: A 173 ASN cc_start: 0.8310 (t0) cc_final: 0.7963 (t0) REVERT: A 254 ARG cc_start: 0.6744 (mpt90) cc_final: 0.6510 (mmp-170) outliers start: 9 outliers final: 4 residues processed: 41 average time/residue: 1.6002 time to fit residues: 66.6034 Evaluate side-chains 43 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 244 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 0.0070 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- 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: 0.8550 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2110 Z= 0.175 Angle : 0.528 8.501 2860 Z= 0.280 Chirality : 0.044 0.132 315 Planarity : 0.004 0.035 376 Dihedral : 4.262 14.846 292 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.80 % Allowed : 15.89 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.61 (0.50), residues: 259 helix: 2.70 (0.57), residues: 87 sheet: -0.44 (0.67), residues: 56 loop : -0.97 (0.47), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 96 HIS 0.005 0.001 HIS A 199 PHE 0.013 0.002 PHE A 259 TYR 0.006 0.001 TYR A 131 ARG 0.003 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.236 Fit side-chains REVERT: A 25 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8211 (tp) REVERT: A 30 ARG cc_start: 0.7485 (ttm-80) cc_final: 0.7187 (ttp-170) REVERT: A 57 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6887 (mp10) REVERT: A 74 MET cc_start: 0.7769 (mtm) cc_final: 0.7489 (pp-130) REVERT: A 173 ASN cc_start: 0.8363 (t0) cc_final: 0.8054 (t0) outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 1.8285 time to fit residues: 74.1568 Evaluate side-chains 42 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 244 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 30.0000 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.8599 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2110 Z= 0.303 Angle : 0.646 8.947 2860 Z= 0.344 Chirality : 0.049 0.152 315 Planarity : 0.005 0.038 376 Dihedral : 4.658 16.032 292 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.21 % Allowed : 15.42 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.39 (0.50), residues: 259 helix: 2.47 (0.57), residues: 86 sheet: -0.57 (0.66), residues: 56 loop : -1.01 (0.47), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 96 HIS 0.004 0.001 HIS A 7 PHE 0.020 0.002 PHE A 259 TYR 0.010 0.002 TYR A 131 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.243 Fit side-chains REVERT: A 25 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8207 (tp) REVERT: A 57 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.6903 (mp10) REVERT: A 74 MET cc_start: 0.7783 (mtm) cc_final: 0.7517 (pp-130) REVERT: A 173 ASN cc_start: 0.8361 (t0) cc_final: 0.7997 (t0) REVERT: A 254 ARG cc_start: 0.6767 (mpt90) cc_final: 0.6543 (mmp-170) outliers start: 9 outliers final: 4 residues processed: 44 average time/residue: 1.7770 time to fit residues: 79.2938 Evaluate side-chains 45 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.8590 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2110 Z= 0.272 Angle : 0.632 9.607 2860 Z= 0.332 Chirality : 0.047 0.146 315 Planarity : 0.005 0.039 376 Dihedral : 4.567 15.984 292 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.27 % Allowed : 16.36 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.39 (0.50), residues: 259 helix: 2.51 (0.57), residues: 86 sheet: -0.61 (0.66), residues: 56 loop : -1.04 (0.47), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 96 HIS 0.006 0.001 HIS A 7 PHE 0.019 0.002 PHE A 259 TYR 0.008 0.002 TYR A 131 ARG 0.003 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.182 Fit side-chains REVERT: A 25 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8206 (tp) REVERT: A 57 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.6903 (mp10) REVERT: A 74 MET cc_start: 0.7754 (mtm) cc_final: 0.7531 (pp-130) REVERT: A 173 ASN cc_start: 0.8299 (t0) cc_final: 0.8005 (t0) REVERT: A 254 ARG cc_start: 0.6774 (mpt90) cc_final: 0.6553 (mmp-170) outliers start: 7 outliers final: 4 residues processed: 42 average time/residue: 1.6510 time to fit residues: 70.3413 Evaluate side-chains 43 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.8597 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2110 Z= 0.281 Angle : 0.644 8.821 2860 Z= 0.343 Chirality : 0.048 0.146 315 Planarity : 0.005 0.042 376 Dihedral : 4.634 16.135 292 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.80 % Allowed : 17.29 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.31 (0.50), residues: 259 helix: 2.37 (0.57), residues: 87 sheet: -0.65 (0.66), residues: 56 loop : -1.05 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 96 HIS 0.004 0.001 HIS A 199 PHE 0.019 0.002 PHE A 259 TYR 0.010 0.002 TYR A 131 ARG 0.002 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.185 Fit side-chains REVERT: A 25 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8207 (tp) REVERT: A 57 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.6905 (mp10) REVERT: A 74 MET cc_start: 0.7801 (mtm) cc_final: 0.7499 (pp-130) REVERT: A 173 ASN cc_start: 0.8315 (t0) cc_final: 0.8001 (t0) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 1.6677 time to fit residues: 72.6717 Evaluate side-chains 45 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8517 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2110 Z= 0.138 Angle : 0.502 9.049 2860 Z= 0.262 Chirality : 0.042 0.135 315 Planarity : 0.004 0.035 376 Dihedral : 4.002 14.161 292 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.34 % Allowed : 17.29 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 0.72 (0.51), residues: 259 helix: 2.89 (0.57), residues: 87 sheet: -0.56 (0.67), residues: 58 loop : -0.88 (0.48), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 96 HIS 0.005 0.001 HIS A 199 PHE 0.009 0.001 PHE A 259 TYR 0.005 0.001 TYR A 131 ARG 0.005 0.000 ARG A 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.234 Fit side-chains REVERT: A 74 MET cc_start: 0.7746 (mtm) cc_final: 0.7500 (pp-130) REVERT: A 173 ASN cc_start: 0.8311 (t0) cc_final: 0.8022 (t0) outliers start: 5 outliers final: 3 residues processed: 43 average time/residue: 1.7592 time to fit residues: 76.6881 Evaluate side-chains 41 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 244 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 0.0000 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 0.4980 chunk 25 optimal weight: 0.0470 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 overall best weight: 0.5284 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.144368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116584 restraints weight = 2279.542| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.69 r_work: 0.3269 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 2110 Z= 0.122 Angle : 0.456 8.462 2860 Z= 0.233 Chirality : 0.041 0.128 315 Planarity : 0.004 0.035 376 Dihedral : 3.511 12.177 292 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.47 % Allowed : 18.22 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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 (0.51), residues: 259 helix: 3.25 (0.56), residues: 86 sheet: -0.57 (0.68), residues: 60 loop : -0.69 (0.48), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 17 HIS 0.005 0.001 HIS A 199 PHE 0.009 0.001 PHE A 92 TYR 0.004 0.000 TYR A 131 ARG 0.007 0.000 ARG A 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1632.30 seconds wall clock time: 33 minutes 9.99 seconds (1989.99 seconds total)