Starting phenix.real_space_refine on Mon Jan 13 13:20:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4n_42974/01_2025/8v4n_42974.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4n_42974/01_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_42974/01_2025/8v4n_42974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4n_42974/01_2025/8v4n_42974.map" model { file = "/net/cci-nas-00/data/ceres_data/8v4n_42974/01_2025/8v4n_42974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4n_42974/01_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-5571/modules/chem_data/mon_lib" Total number of atoms: 2067 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2067 Classifications: {'peptide': 263} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Time building chain proxies: 2.88, per 1000 atoms: 1.39 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 241.4 milliseconds 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 482 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 3 sheets defined 36.5% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 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: 0.55 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: 2.270 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: 11.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.880 ------------------------------------------------------------------------------- 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 : 0.269 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: 1.7531 time to fit residues: 90.7532 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 : 0.244 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105853 restraints weight = 2254.128| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.77 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: 0.2244 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 to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.265 Fit side-chains REVERT: A 25 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8296 (tp) REVERT: A 57 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.6927 (mp10) REVERT: A 74 MET cc_start: 0.8323 (mtm) cc_final: 0.7709 (pp-130) REVERT: A 173 ASN cc_start: 0.8340 (t0) cc_final: 0.7946 (t0) outliers start: 6 outliers final: 2 residues processed: 41 average time/residue: 1.8703 time to fit residues: 77.7552 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 : 0.315 ------------------------------------------------------------------------------- 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: 10.0000 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.0470 chunk 5 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 overall best weight: 1.8082 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.140718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.110524 restraints weight = 2267.424| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.77 r_work: 0.3182 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2110 Z= 0.145 Angle : 0.489 7.563 2860 Z= 0.260 Chirality : 0.043 0.130 315 Planarity : 0.004 0.031 376 Dihedral : 4.148 17.086 292 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.80 % Allowed : 14.02 % 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: 0.75 (0.52), residues: 259 helix: 2.76 (0.56), residues: 87 sheet: -0.62 (0.69), residues: 60 loop : -0.66 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 96 HIS 0.006 0.001 HIS A 199 PHE 0.011 0.001 PHE A 259 TYR 0.005 0.001 TYR A 131 ARG 0.002 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 44 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.249 Fit side-chains REVERT: A 57 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.6771 (mp10) REVERT: A 74 MET cc_start: 0.8316 (mtm) cc_final: 0.7725 (pp-130) REVERT: A 173 ASN cc_start: 0.8277 (t0) cc_final: 0.7949 (t0) outliers start: 6 outliers final: 3 residues processed: 39 average time/residue: 1.9374 time to fit residues: 76.6335 Evaluate side-chains 40 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 3 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 0.0050 chunk 14 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.135552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105202 restraints weight = 2210.633| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.74 r_work: 0.3111 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2110 Z= 0.273 Angle : 0.618 8.323 2860 Z= 0.329 Chirality : 0.048 0.143 315 Planarity : 0.005 0.033 376 Dihedral : 4.603 15.220 292 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: 0.46 (0.51), residues: 259 helix: 2.41 (0.57), residues: 87 sheet: -0.75 (0.68), residues: 60 loop : -0.75 (0.50), 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 7 PHE 0.018 0.002 PHE A 259 TYR 0.009 0.001 TYR A 131 ARG 0.002 0.000 ARG A 234 *********************** 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 45 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.254 Fit side-chains REVERT: A 25 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8256 (tp) REVERT: A 57 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7004 (mp10) REVERT: A 74 MET cc_start: 0.8317 (mtm) cc_final: 0.7674 (pp-130) REVERT: A 173 ASN cc_start: 0.8354 (t0) cc_final: 0.8008 (t0) REVERT: A 199 HIS cc_start: 0.5763 (p-80) cc_final: 0.4393 (t70) outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 1.8876 time to fit residues: 80.5185 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 : 0.231 ------------------------------------------------------------------------------- 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: 9.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.137084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106943 restraints weight = 2246.711| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.75 r_work: 0.3133 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2110 Z= 0.206 Angle : 0.556 8.285 2860 Z= 0.296 Chirality : 0.045 0.133 315 Planarity : 0.005 0.034 376 Dihedral : 4.374 14.815 292 Min Nonbonded Distance : 2.657 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: 0.58 (0.51), residues: 259 helix: 2.52 (0.57), residues: 87 sheet: -0.41 (0.70), residues: 56 loop : -0.87 (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 0.016 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 to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.247 Fit side-chains REVERT: A 25 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8238 (tp) REVERT: A 57 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.6929 (mp10) REVERT: A 74 MET cc_start: 0.8317 (mtm) cc_final: 0.7702 (pp-130) REVERT: A 173 ASN cc_start: 0.8317 (t0) cc_final: 0.7995 (t0) REVERT: A 199 HIS cc_start: 0.5812 (p-80) cc_final: 0.4285 (t70) outliers start: 7 outliers final: 3 residues processed: 40 average time/residue: 1.9660 time to fit residues: 79.8170 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 : 0.224 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.104379 restraints weight = 2260.128| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.75 r_work: 0.3100 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2110 Z= 0.291 Angle : 0.638 8.732 2860 Z= 0.340 Chirality : 0.048 0.149 315 Planarity : 0.005 0.037 376 Dihedral : 4.662 15.947 292 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.80 % Allowed : 16.82 % 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: 0.37 (0.50), residues: 259 helix: 2.31 (0.57), residues: 87 sheet: -0.51 (0.68), residues: 56 loop : -0.97 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 96 HIS 0.005 0.002 HIS A 7 PHE 0.019 0.002 PHE A 259 TYR 0.010 0.002 TYR A 131 ARG 0.003 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 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: 6 poor density : 37 time to evaluate : 0.251 Fit side-chains REVERT: A 25 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8274 (tp) REVERT: A 57 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.6931 (mp10) REVERT: A 74 MET cc_start: 0.8317 (mtm) cc_final: 0.7710 (pp-130) REVERT: A 173 ASN cc_start: 0.8367 (t0) cc_final: 0.8005 (t0) REVERT: A 254 ARG cc_start: 0.6951 (mpt90) cc_final: 0.6702 (mmp-170) outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 1.9260 time to fit residues: 78.1085 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 : 0.249 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 0.0270 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 overall best weight: 3.4046 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.136311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106403 restraints weight = 2285.654| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.75 r_work: 0.3125 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2574 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= 0.211 Angle : 0.567 8.916 2860 Z= 0.301 Chirality : 0.045 0.134 315 Planarity : 0.005 0.035 376 Dihedral : 4.420 15.642 292 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.27 % Allowed : 16.36 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.50), residues: 259 helix: 2.47 (0.57), residues: 87 sheet: -0.53 (0.68), residues: 56 loop : -0.94 (0.48), 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 0.015 0.002 PHE A 259 TYR 0.007 0.001 TYR A 131 ARG 0.003 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 to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.233 Fit side-chains REVERT: A 25 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8258 (tp) REVERT: A 57 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.6921 (mp10) REVERT: A 74 MET cc_start: 0.8329 (mtm) cc_final: 0.7701 (pp-130) REVERT: A 173 ASN cc_start: 0.8342 (t0) cc_final: 0.8022 (t0) REVERT: A 254 ARG cc_start: 0.6922 (mpt90) cc_final: 0.6663 (mmp-170) outliers start: 7 outliers final: 5 residues processed: 39 average time/residue: 1.9687 time to fit residues: 77.8655 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 : 0.374 ------------------------------------------------------------------------------- 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 171 LYS Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.137709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107932 restraints weight = 2326.307| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.76 r_work: 0.3146 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2110 Z= 0.177 Angle : 0.531 9.063 2860 Z= 0.281 Chirality : 0.044 0.132 315 Planarity : 0.004 0.033 376 Dihedral : 4.199 14.988 292 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: 0.63 (0.51), residues: 259 helix: 2.66 (0.57), residues: 87 sheet: -0.48 (0.68), residues: 56 loop : -0.87 (0.48), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 96 HIS 0.005 0.001 HIS A 199 PHE 0.013 0.001 PHE A 259 TYR 0.006 0.001 TYR A 131 ARG 0.004 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.247 Fit side-chains REVERT: A 25 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8239 (tp) REVERT: A 57 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: A 74 MET cc_start: 0.8297 (mtm) cc_final: 0.7676 (pp-130) REVERT: A 173 ASN cc_start: 0.8369 (t0) cc_final: 0.8060 (t0) outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 2.0462 time to fit residues: 85.0504 Evaluate side-chains 44 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.138695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109130 restraints weight = 2310.634| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.75 r_work: 0.3161 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2110 Z= 0.162 Angle : 0.516 8.963 2860 Z= 0.271 Chirality : 0.043 0.131 315 Planarity : 0.004 0.032 376 Dihedral : 4.075 14.610 292 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: 0.78 (0.51), residues: 259 helix: 2.81 (0.57), residues: 87 sheet: -0.41 (0.70), residues: 56 loop : -0.81 (0.49), 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 199 PHE 0.012 0.001 PHE A 259 TYR 0.006 0.001 TYR A 131 ARG 0.004 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 44 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.238 Fit side-chains REVERT: A 25 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8227 (tp) REVERT: A 57 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.6916 (mp10) REVERT: A 74 MET cc_start: 0.8275 (mtm) cc_final: 0.7683 (pp-130) REVERT: A 173 ASN cc_start: 0.8399 (t0) cc_final: 0.8081 (t0) outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 1.9480 time to fit residues: 79.1179 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 : 0.245 ------------------------------------------------------------------------------- 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 171 LYS Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.136747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107216 restraints weight = 2235.736| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.72 r_work: 0.3139 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2588 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= 0.197 Angle : 0.558 9.148 2860 Z= 0.292 Chirality : 0.045 0.135 315 Planarity : 0.005 0.045 376 Dihedral : 4.239 15.064 292 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.80 % Allowed : 16.82 % 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: 0.66 (0.51), residues: 259 helix: 2.68 (0.57), residues: 87 sheet: -0.47 (0.69), residues: 56 loop : -0.84 (0.49), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 96 HIS 0.004 0.001 HIS A 199 PHE 0.014 0.002 PHE A 259 TYR 0.007 0.001 TYR A 131 ARG 0.006 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 43 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.237 Fit side-chains REVERT: A 25 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8237 (tp) REVERT: A 57 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6924 (mp10) REVERT: A 74 MET cc_start: 0.8299 (mtm) cc_final: 0.7667 (pp-130) REVERT: A 173 ASN cc_start: 0.8409 (t0) cc_final: 0.8086 (t0) outliers start: 6 outliers final: 4 residues processed: 40 average time/residue: 1.9132 time to fit residues: 77.6190 Evaluate side-chains 43 residues out of total 214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.139490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110225 restraints weight = 2271.365| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.73 r_work: 0.3179 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2453 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= 0.149 Angle : 0.509 9.037 2860 Z= 0.265 Chirality : 0.043 0.130 315 Planarity : 0.004 0.040 376 Dihedral : 3.965 14.135 292 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.27 % Allowed : 16.36 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.51), residues: 259 helix: 2.90 (0.56), residues: 87 sheet: -0.36 (0.70), residues: 56 loop : -0.75 (0.49), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 96 HIS 0.004 0.001 HIS A 199 PHE 0.010 0.001 PHE A 259 TYR 0.004 0.001 TYR A 190 ARG 0.007 0.000 ARG A 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2917.37 seconds wall clock time: 52 minutes 48.51 seconds (3168.51 seconds total)