Starting phenix.real_space_refine on Wed Mar 5 14:50:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4n_42974/03_2025/8v4n_42974.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4n_42974/03_2025/8v4n_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/cci-nas-00/data/ceres_data/8v4n_42974/03_2025/8v4n_42974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4n_42974/03_2025/8v4n_42974.map" model { file = "/net/cci-nas-00/data/ceres_data/8v4n_42974/03_2025/8v4n_42974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4n_42974/03_2025/8v4n_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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.69, per 1000 atoms: 1.79 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 218.2 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: 0.24 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: 0.44 Time building geometry restraints manager: 0.58 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: 0.00 - 1.00: 2723 1.00 - 2.01: 103 2.01 - 3.01: 29 3.01 - 4.02: 3 4.02 - 5.02: 2 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: 2.290 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.250 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:14.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.220 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.199 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: 1.7212 time to fit residues: 89.0445 Evaluate side-chains 41 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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: 3.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.136195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105387 restraints weight = 2253.424| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.76 r_work: 0.3109 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2252 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= 0.272 Angle : 0.632 7.565 2860 Z= 0.337 Chirality : 0.048 0.163 315 Planarity : 0.005 0.034 376 Dihedral : 4.707 21.642 292 Min Nonbonded Distance : 2.640 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: 0.63 (0.51), residues: 259 helix: 2.42 (0.56), residues: 87 sheet: -0.28 (0.71), residues: 56 loop : -0.78 (0.50), residues: 116 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 0.018 0.002 PHE A 259 TYR 0.009 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 to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.246 Fit side-chains REVERT: A 25 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8302 (tp) REVERT: A 57 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.6930 (mp10) REVERT: A 74 MET cc_start: 0.8327 (mtm) cc_final: 0.7718 (pp-130) REVERT: A 173 ASN cc_start: 0.8348 (t0) cc_final: 0.7950 (t0) outliers start: 6 outliers final: 2 residues processed: 41 average time/residue: 1.8761 time to fit residues: 78.0469 Evaluate side-chains 43 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 18 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.142388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112289 restraints weight = 2276.291| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.77 r_work: 0.3207 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1925 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= 0.132 Angle : 0.466 7.556 2860 Z= 0.248 Chirality : 0.042 0.130 315 Planarity : 0.004 0.030 376 Dihedral : 4.044 17.291 292 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.87 % Allowed : 14.95 % Favored : 83.18 % 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 (0.52), residues: 259 helix: 2.84 (0.56), residues: 87 sheet: -0.57 (0.70), residues: 60 loop : -0.63 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 96 HIS 0.007 0.001 HIS A 199 PHE 0.008 0.001 PHE A 259 TYR 0.005 0.001 TYR A 131 ARG 0.003 0.000 ARG A 30 *********************** 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 43 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.230 Fit side-chains REVERT: A 30 ARG cc_start: 0.7253 (ttm-80) cc_final: 0.6993 (ttp-170) REVERT: A 57 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: A 74 MET cc_start: 0.8267 (mtm) cc_final: 0.7683 (pp-130) REVERT: A 173 ASN cc_start: 0.8249 (t0) cc_final: 0.7946 (t0) REVERT: A 244 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7736 (m-30) outliers start: 4 outliers final: 0 residues processed: 40 average time/residue: 1.9497 time to fit residues: 79.0738 Evaluate side-chains 39 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLN 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 3 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 14 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.136548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.106251 restraints weight = 2206.786| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.73 r_work: 0.3124 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2110 Z= 0.234 Angle : 0.578 8.142 2860 Z= 0.308 Chirality : 0.046 0.137 315 Planarity : 0.005 0.032 376 Dihedral : 4.453 15.363 292 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.34 % Allowed : 15.89 % 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: 0.57 (0.51), residues: 259 helix: 2.53 (0.57), residues: 87 sheet: -0.73 (0.68), residues: 60 loop : -0.70 (0.50), residues: 112 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 0.016 0.002 PHE A 259 TYR 0.009 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 43 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.227 Fit side-chains REVERT: A 25 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8258 (tp) REVERT: A 30 ARG cc_start: 0.7607 (ttm-80) cc_final: 0.7359 (ttm110) REVERT: A 57 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.6943 (mp10) REVERT: A 74 MET cc_start: 0.8308 (mtm) cc_final: 0.7676 (pp-130) REVERT: A 173 ASN cc_start: 0.8391 (t0) cc_final: 0.8010 (t0) REVERT: A 199 HIS cc_start: 0.5804 (p-80) cc_final: 0.4460 (t70) outliers start: 5 outliers final: 2 residues processed: 39 average time/residue: 1.9302 time to fit residues: 76.4056 Evaluate side-chains 42 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 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 = 0.3638 r_free = 0.3638 target = 0.138009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107857 restraints weight = 2251.356| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.75 r_work: 0.3146 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2355 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= 0.185 Angle : 0.531 8.140 2860 Z= 0.283 Chirality : 0.044 0.132 315 Planarity : 0.004 0.032 376 Dihedral : 4.263 14.531 292 Min Nonbonded Distance : 2.656 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: 0.59 (0.51), residues: 259 helix: 2.60 (0.56), residues: 87 sheet: -0.72 (0.68), residues: 60 loop : -0.73 (0.49), residues: 112 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 0.014 0.002 PHE A 259 TYR 0.006 0.001 TYR A 131 ARG 0.001 0.000 ARG A 254 *********************** 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 44 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.261 Fit side-chains REVERT: A 25 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8230 (tp) REVERT: A 30 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7293 (ttm110) REVERT: A 57 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: A 74 MET cc_start: 0.8298 (mtm) cc_final: 0.7644 (pp-130) REVERT: A 173 ASN cc_start: 0.8369 (t0) cc_final: 0.8036 (t0) REVERT: A 199 HIS cc_start: 0.5759 (p-80) cc_final: 0.4405 (t70) outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 1.9545 time to fit residues: 79.3495 Evaluate side-chains 43 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 171 LYS 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 0 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 25 optimal weight: 0.0770 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.137685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.107650 restraints weight = 2257.575| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.74 r_work: 0.3146 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2110 Z= 0.186 Angle : 0.539 8.532 2860 Z= 0.284 Chirality : 0.045 0.134 315 Planarity : 0.004 0.032 376 Dihedral : 4.222 14.359 292 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.27 % Allowed : 15.42 % 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: 0.68 (0.51), residues: 259 helix: 2.63 (0.56), residues: 87 sheet: -0.41 (0.70), residues: 56 loop : -0.80 (0.49), 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 0.014 0.002 PHE A 259 TYR 0.007 0.001 TYR A 131 ARG 0.001 0.000 ARG A 254 *********************** 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 to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.242 Fit side-chains REVERT: A 25 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8280 (tp) REVERT: A 57 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.6937 (mp10) REVERT: A 74 MET cc_start: 0.8315 (mtm) cc_final: 0.7682 (pp-130) REVERT: A 173 ASN cc_start: 0.8424 (t0) cc_final: 0.8094 (t0) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 1.9498 time to fit residues: 77.1168 Evaluate side-chains 42 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 2 optimal weight: 0.0470 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.135952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.105829 restraints weight = 2282.382| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.75 r_work: 0.3118 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2110 Z= 0.235 Angle : 0.586 8.874 2860 Z= 0.310 Chirality : 0.046 0.137 315 Planarity : 0.004 0.034 376 Dihedral : 4.427 15.379 292 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: 0.55 (0.51), residues: 259 helix: 2.49 (0.57), residues: 87 sheet: -0.46 (0.69), residues: 56 loop : -0.86 (0.49), 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 7 PHE 0.017 0.002 PHE A 259 TYR 0.009 0.001 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 45 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.248 Fit side-chains REVERT: A 25 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8220 (tp) REVERT: A 57 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.6968 (mp10) REVERT: A 74 MET cc_start: 0.8306 (mtm) cc_final: 0.7689 (pp-130) REVERT: A 173 ASN cc_start: 0.8362 (t0) cc_final: 0.8024 (t0) REVERT: A 254 ARG cc_start: 0.7010 (mpt90) cc_final: 0.6749 (mmp-170) outliers start: 7 outliers final: 3 residues processed: 42 average time/residue: 1.8526 time to fit residues: 78.9716 Evaluate side-chains 42 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.141070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.111521 restraints weight = 2320.906| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.76 r_work: 0.3196 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 2110 Z= 0.129 Angle : 0.480 8.819 2860 Z= 0.249 Chirality : 0.042 0.132 315 Planarity : 0.004 0.031 376 Dihedral : 3.864 13.243 292 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: 0.89 (0.51), residues: 259 helix: 2.88 (0.56), residues: 87 sheet: -0.37 (0.70), residues: 56 loop : -0.71 (0.49), 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 0.009 0.001 PHE A 92 TYR 0.004 0.001 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 39 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.381 Fit side-chains REVERT: A 30 ARG cc_start: 0.7492 (ttm-80) cc_final: 0.7208 (ttp-170) REVERT: A 74 MET cc_start: 0.8259 (mtm) cc_final: 0.7673 (pp-130) REVERT: A 173 ASN cc_start: 0.8303 (t0) cc_final: 0.8000 (t0) REVERT: A 244 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7709 (m-30) outliers start: 4 outliers final: 1 residues processed: 37 average time/residue: 1.8772 time to fit residues: 70.5004 Evaluate side-chains 37 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 244 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 1 optimal weight: 0.0980 chunk 14 optimal weight: 0.0570 chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.145874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117074 restraints weight = 2329.592| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.76 r_work: 0.3273 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 2110 Z= 0.117 Angle : 0.445 8.698 2860 Z= 0.227 Chirality : 0.041 0.127 315 Planarity : 0.004 0.029 376 Dihedral : 3.482 11.578 292 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: 1.07 (0.51), residues: 259 helix: 3.04 (0.56), residues: 88 sheet: -0.25 (0.70), residues: 56 loop : -0.65 (0.49), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 96 HIS 0.005 0.001 HIS A 199 PHE 0.009 0.001 PHE A 92 TYR 0.004 0.000 TYR A 131 ARG 0.001 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 37 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.242 Fit side-chains REVERT: A 9 GLU cc_start: 0.7622 (mt-10) cc_final: 0.6802 (tp30) REVERT: A 30 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.6975 (ttp-170) REVERT: A 74 MET cc_start: 0.8225 (mtm) cc_final: 0.7632 (pp-130) REVERT: A 173 ASN cc_start: 0.8349 (t0) cc_final: 0.8107 (t0) outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 1.9441 time to fit residues: 72.9798 Evaluate side-chains 36 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.135253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105599 restraints weight = 2232.010| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.72 r_work: 0.3114 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2704 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= 0.278 Angle : 0.629 9.434 2860 Z= 0.330 Chirality : 0.048 0.146 315 Planarity : 0.005 0.033 376 Dihedral : 4.426 15.556 292 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.47 % Allowed : 16.82 % 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: 0.74 (0.51), residues: 259 helix: 2.69 (0.57), residues: 86 sheet: -0.41 (0.69), residues: 56 loop : -0.73 (0.49), 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 0.018 0.002 PHE A 259 TYR 0.009 0.001 TYR A 131 ARG 0.005 0.001 ARG A 170 ********************** 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 39 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.285 Fit side-chains REVERT: A 74 MET cc_start: 0.8318 (mtm) cc_final: 0.7669 (pp-130) REVERT: A 173 ASN cc_start: 0.8437 (t0) cc_final: 0.8075 (t0) REVERT: A 254 ARG cc_start: 0.6993 (mpt90) cc_final: 0.6733 (mmp-170) outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 2.0193 time to fit residues: 79.8707 Evaluate side-chains 38 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.140380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111026 restraints weight = 2265.508| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.73 r_work: 0.3190 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2395 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= 0.140 Angle : 0.497 9.113 2860 Z= 0.257 Chirality : 0.043 0.130 315 Planarity : 0.004 0.031 376 Dihedral : 3.908 13.676 292 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.47 % Allowed : 18.69 % 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: 0.90 (0.52), residues: 259 helix: 2.95 (0.56), residues: 87 sheet: -0.50 (0.69), residues: 58 loop : -0.67 (0.50), residues: 114 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 0.009 0.001 PHE A 259 TYR 0.005 0.001 TYR A 131 ARG 0.005 0.000 ARG A 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3036.94 seconds wall clock time: 52 minutes 30.01 seconds (3150.01 seconds total)