Starting phenix.real_space_refine on Fri Aug 2 12:55:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4n_42974/08_2024/8v4n_42974.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4n_42974/08_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_42974/08_2024/8v4n_42974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4n_42974/08_2024/8v4n_42974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4n_42974/08_2024/8v4n_42974.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4n_42974/08_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-5409/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: 3.47, per 1000 atoms: 1.68 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: 0.64 Conformation dependent library (CDL) restraints added in 433.9 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: 0.23 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: 0.49 Time building geometry restraints manager: 0.74 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 3.120 nonbonded pdb=" N GLY A 159 " pdb=" OE2 GLU A 204 " model vdw 2.333 3.120 nonbonded pdb=" OD1 ASN A 10 " pdb=" NE1 TRP A 17 " model vdw 2.442 3.120 nonbonded pdb=" N GLU A 15 " pdb=" OE1 GLU A 15 " model vdw 2.588 3.120 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: 2.980 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.860 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:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.500 ------------------------------------------------------------------------------- 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 : 0.221 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: 1.5608 time to fit residues: 80.7988 Evaluate side-chains 41 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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: 0.8566 moved from start: 0.2244 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= 0.249 Angle : 0.611 7.283 2860 Z= 0.324 Chirality : 0.047 0.149 315 Planarity : 0.005 0.034 376 Dihedral : 4.644 21.234 292 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 1.22 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: 0.67 (0.51), residues: 259 helix: 2.56 (0.56), residues: 86 sheet: -0.30 (0.71), residues: 56 loop : -0.78 (0.50), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 96 HIS 0.008 0.002 HIS A 199 PHE 0.017 0.002 PHE A 259 TYR 0.008 0.001 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 45 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.242 Fit side-chains REVERT: A 25 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8236 (tp) REVERT: A 57 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.6874 (mp10) REVERT: A 74 MET cc_start: 0.7790 (mtm) cc_final: 0.7477 (pp-130) REVERT: A 173 ASN cc_start: 0.8336 (t0) cc_final: 0.7938 (t0) outliers start: 6 outliers final: 2 residues processed: 41 average time/residue: 1.7951 time to fit residues: 74.6944 Evaluate side-chains 43 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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: 4.9990 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 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: 0.8574 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2110 Z= 0.242 Angle : 0.596 7.802 2860 Z= 0.318 Chirality : 0.047 0.137 315 Planarity : 0.005 0.034 376 Dihedral : 4.620 17.574 292 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.80 % Allowed : 14.49 % Favored : 82.71 % 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: 0.48 (0.51), residues: 259 helix: 2.41 (0.57), residues: 87 sheet: -0.73 (0.68), residues: 60 loop : -0.74 (0.49), residues: 112 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 0.017 0.002 PHE A 259 TYR 0.008 0.001 TYR A 131 ARG 0.002 0.000 ARG A 103 *********************** 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 46 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.254 Fit side-chains REVERT: A 19 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7479 (ttp-110) REVERT: A 25 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8219 (tp) REVERT: A 57 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.6981 (mp10) REVERT: A 74 MET cc_start: 0.7763 (mtm) cc_final: 0.7465 (pp-130) REVERT: A 173 ASN cc_start: 0.8328 (t0) cc_final: 0.7959 (t0) REVERT: A 199 HIS cc_start: 0.5826 (p-80) cc_final: 0.4442 (t70) outliers start: 6 outliers final: 2 residues processed: 41 average time/residue: 1.8508 time to fit residues: 77.0305 Evaluate side-chains 42 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- 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: 0.8586 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2110 Z= 0.260 Angle : 0.611 8.159 2860 Z= 0.327 Chirality : 0.048 0.139 315 Planarity : 0.005 0.036 376 Dihedral : 4.642 15.257 292 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.21 % Allowed : 14.49 % 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: 0.46 (0.50), residues: 259 helix: 2.37 (0.57), residues: 87 sheet: -0.42 (0.69), residues: 56 loop : -0.93 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 96 HIS 0.006 0.001 HIS A 7 PHE 0.018 0.002 PHE A 259 TYR 0.008 0.001 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 48 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.220 Fit side-chains REVERT: A 19 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7620 (ttp-110) REVERT: A 25 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8223 (tp) REVERT: A 57 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.6900 (mp10) REVERT: A 74 MET cc_start: 0.7779 (mtm) cc_final: 0.7483 (pp-130) REVERT: A 173 ASN cc_start: 0.8324 (t0) cc_final: 0.7960 (t0) REVERT: A 199 HIS cc_start: 0.5888 (p-80) cc_final: 0.4274 (t70) outliers start: 9 outliers final: 3 residues processed: 42 average time/residue: 1.8336 time to fit residues: 78.0836 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 19 ARG 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 Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 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: 0.8563 moved from start: 0.2477 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= 0.202 Angle : 0.554 8.349 2860 Z= 0.295 Chirality : 0.045 0.133 315 Planarity : 0.005 0.034 376 Dihedral : 4.394 14.879 292 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.74 % Allowed : 15.89 % 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: 0.58 (0.51), residues: 259 helix: 2.56 (0.57), residues: 87 sheet: -0.41 (0.70), residues: 56 loop : -0.92 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 96 HIS 0.005 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 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 45 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.256 Fit side-chains REVERT: A 19 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7455 (ttp-110) REVERT: A 25 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8209 (tp) REVERT: A 57 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.6891 (mp10) REVERT: A 74 MET cc_start: 0.7778 (mtm) cc_final: 0.7496 (pp-130) REVERT: A 173 ASN cc_start: 0.8296 (t0) cc_final: 0.7970 (t0) outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 1.9336 time to fit residues: 78.4392 Evaluate side-chains 44 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG 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 Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 18 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- 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: 0.8470 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2110 Z= 0.123 Angle : 0.456 8.411 2860 Z= 0.240 Chirality : 0.042 0.131 315 Planarity : 0.004 0.030 376 Dihedral : 3.813 12.638 292 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.80 % Allowed : 16.36 % 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: 0.96 (0.52), residues: 259 helix: 2.99 (0.57), residues: 87 sheet: -0.20 (0.72), residues: 56 loop : -0.78 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 96 HIS 0.005 0.001 HIS A 199 PHE 0.008 0.001 PHE A 92 TYR 0.004 0.001 TYR A 131 ARG 0.004 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 41 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.223 Fit side-chains REVERT: A 74 MET cc_start: 0.7698 (mtm) cc_final: 0.7486 (pp-130) REVERT: A 173 ASN cc_start: 0.8315 (t0) cc_final: 0.8029 (t0) REVERT: A 244 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7673 (m-30) outliers start: 6 outliers final: 1 residues processed: 37 average time/residue: 1.8048 time to fit residues: 67.7597 Evaluate side-chains 37 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL 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: 3.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2110 Z= 0.319 Angle : 0.658 8.962 2860 Z= 0.349 Chirality : 0.049 0.153 315 Planarity : 0.005 0.035 376 Dihedral : 4.617 15.889 292 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: 0.52 (0.51), residues: 259 helix: 2.48 (0.57), residues: 87 sheet: -0.44 (0.69), residues: 56 loop : -0.92 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.004 0.000 ARG A 30 *********************** 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 43 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.257 Fit side-chains REVERT: A 74 MET cc_start: 0.7796 (mtm) cc_final: 0.7479 (pp-130) REVERT: A 173 ASN cc_start: 0.8371 (t0) cc_final: 0.8005 (t0) outliers start: 6 outliers final: 4 residues processed: 40 average time/residue: 1.9108 time to fit residues: 77.5167 Evaluate side-chains 41 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ARG 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: 8.9990 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.8605 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2110 Z= 0.331 Angle : 0.683 9.316 2860 Z= 0.364 Chirality : 0.050 0.157 315 Planarity : 0.006 0.037 376 Dihedral : 4.828 17.028 292 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.27 % Allowed : 15.89 % 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: 0.27 (0.50), residues: 259 helix: 2.27 (0.57), residues: 86 sheet: -0.60 (0.66), residues: 56 loop : -1.03 (0.48), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 96 HIS 0.007 0.001 HIS A 7 PHE 0.022 0.002 PHE A 259 TYR 0.011 0.002 TYR A 131 ARG 0.003 0.000 ARG A 103 *********************** 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 44 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.244 Fit side-chains REVERT: A 74 MET cc_start: 0.7722 (mtm) cc_final: 0.7469 (pp-130) REVERT: A 173 ASN cc_start: 0.8288 (t0) cc_final: 0.7983 (t0) REVERT: A 254 ARG cc_start: 0.6764 (mpt90) cc_final: 0.6555 (mmp-170) outliers start: 7 outliers final: 5 residues processed: 40 average time/residue: 1.9401 time to fit residues: 78.7004 Evaluate side-chains 41 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 135 ARG 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: 2.9990 chunk 23 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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: 0.8583 moved from start: 0.2751 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= 0.257 Angle : 0.616 9.204 2860 Z= 0.327 Chirality : 0.047 0.136 315 Planarity : 0.005 0.039 376 Dihedral : 4.561 16.016 292 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.87 % Allowed : 17.29 % 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: 0.39 (0.50), residues: 259 helix: 2.47 (0.57), residues: 87 sheet: -0.63 (0.66), residues: 56 loop : -1.01 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 96 HIS 0.005 0.001 HIS A 7 PHE 0.018 0.002 PHE A 259 TYR 0.009 0.001 TYR A 131 ARG 0.002 0.000 ARG A 103 *********************** 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 39 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.331 Fit side-chains REVERT: A 74 MET cc_start: 0.7750 (mtm) cc_final: 0.7525 (pp-130) REVERT: A 173 ASN cc_start: 0.8330 (t0) cc_final: 0.8007 (t0) REVERT: A 254 ARG cc_start: 0.6731 (mpt90) cc_final: 0.6507 (mmp-170) outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 1.9293 time to fit residues: 72.5240 Evaluate side-chains 38 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0270 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 23 optimal weight: 0.0020 chunk 13 optimal weight: 2.9990 overall best weight: 1.1650 ------------------------------------------------------------------------------- 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: 0.8503 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2110 Z= 0.147 Angle : 0.504 8.986 2860 Z= 0.264 Chirality : 0.042 0.133 315 Planarity : 0.004 0.042 376 Dihedral : 3.976 13.750 292 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.93 % Allowed : 18.69 % 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: 0.83 (0.51), residues: 259 helix: 2.96 (0.56), residues: 87 sheet: -0.42 (0.69), residues: 56 loop : -0.84 (0.48), residues: 116 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 92 TYR 0.004 0.001 TYR A 131 ARG 0.008 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 37 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.282 Fit side-chains REVERT: A 30 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.6975 (ttp-170) REVERT: A 173 ASN cc_start: 0.8290 (t0) cc_final: 0.8011 (t0) REVERT: A 244 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7733 (m-30) REVERT: A 254 ARG cc_start: 0.6691 (mpt90) cc_final: 0.6423 (mmp-170) outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 1.9181 time to fit residues: 72.0591 Evaluate side-chains 37 residues out of total 214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 0 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 0.3980 chunk 10 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.137208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.108218 restraints weight = 2248.748| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.71 r_work: 0.3155 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2110 Z= 0.195 Angle : 0.553 8.927 2860 Z= 0.292 Chirality : 0.045 0.138 315 Planarity : 0.005 0.038 376 Dihedral : 4.215 14.943 292 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.87 % Allowed : 18.22 % 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: 0.71 (0.51), residues: 259 helix: 2.83 (0.56), residues: 87 sheet: -0.48 (0.69), residues: 56 loop : -0.90 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 96 HIS 0.005 0.001 HIS A 199 PHE 0.014 0.002 PHE A 259 TYR 0.007 0.001 TYR A 131 ARG 0.006 0.000 ARG A 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1715.97 seconds wall clock time: 30 minutes 43.96 seconds (1843.96 seconds total)