Starting phenix.real_space_refine on Wed Mar 5 14:16:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p34_17383/03_2025/8p34_17383_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p34_17383/03_2025/8p34_17383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p34_17383/03_2025/8p34_17383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p34_17383/03_2025/8p34_17383.map" model { file = "/net/cci-nas-00/data/ceres_data/8p34_17383/03_2025/8p34_17383_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p34_17383/03_2025/8p34_17383_neut.cif" } resolution = 2.61 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= 0.000 sd= 0.002 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 1 5.16 5 C 445 2.51 5 N 132 2.21 5 O 133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 711 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 711 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Time building chain proxies: 1.13, per 1000 atoms: 1.59 Number of scatterers: 711 At special positions: 0 Unit cell: (116.25, 75.33, 30.69, 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 1 16.00 O 133 8.00 N 132 7.00 C 445 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: 0.36 Conformation dependent library (CDL) restraints added in 271.2 milliseconds 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 162 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 152 1.34 - 1.45: 163 1.45 - 1.57: 406 1.57 - 1.69: 0 1.69 - 1.81: 1 Bond restraints: 722 Sorted by residual: bond pdb=" CA SER A 262 " pdb=" CB SER A 262 " ideal model delta sigma weight residual 1.532 1.488 0.044 1.59e-02 3.96e+03 7.79e+00 bond pdb=" CE1 HIS A 362 " pdb=" NE2 HIS A 362 " ideal model delta sigma weight residual 1.321 1.295 0.026 1.00e-02 1.00e+04 6.54e+00 bond pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 1.354 1.326 0.028 1.10e-02 8.26e+03 6.45e+00 bond pdb=" CA SER A 352 " pdb=" CB SER A 352 " ideal model delta sigma weight residual 1.534 1.495 0.039 1.72e-02 3.38e+03 5.02e+00 bond pdb=" C GLN A 269 " pdb=" O GLN A 269 " ideal model delta sigma weight residual 1.233 1.223 0.010 4.80e-03 4.34e+04 4.30e+00 ... (remaining 717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 649 1.14 - 2.29: 239 2.29 - 3.43: 50 3.43 - 4.57: 18 4.57 - 5.71: 8 Bond angle restraints: 964 Sorted by residual: angle pdb=" C HIS A 268 " pdb=" N GLN A 269 " pdb=" CA GLN A 269 " ideal model delta sigma weight residual 123.10 126.62 -3.52 9.60e-01 1.09e+00 1.35e+01 angle pdb=" CB GLU A 264 " pdb=" CG GLU A 264 " pdb=" CD GLU A 264 " ideal model delta sigma weight residual 112.60 118.31 -5.71 1.70e+00 3.46e-01 1.13e+01 angle pdb=" N LYS A 369 " pdb=" CA LYS A 369 " pdb=" C LYS A 369 " ideal model delta sigma weight residual 108.99 113.92 -4.93 1.57e+00 4.06e-01 9.87e+00 angle pdb=" C ASN A 359 " pdb=" CA ASN A 359 " pdb=" CB ASN A 359 " ideal model delta sigma weight residual 112.11 116.62 -4.51 1.46e+00 4.69e-01 9.53e+00 angle pdb=" CB GLU A 342 " pdb=" CG GLU A 342 " pdb=" CD GLU A 342 " ideal model delta sigma weight residual 112.60 117.71 -5.11 1.70e+00 3.46e-01 9.05e+00 ... (remaining 959 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 9.43: 351 9.43 - 18.85: 64 18.85 - 28.26: 23 28.26 - 37.68: 2 37.68 - 47.10: 2 Dihedral angle restraints: 442 sinusoidal: 186 harmonic: 256 Sorted by residual: dihedral pdb=" CA SER A 356 " pdb=" C SER A 356 " pdb=" N LEU A 357 " pdb=" CA LEU A 357 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA SER A 341 " pdb=" C SER A 341 " pdb=" N GLU A 342 " pdb=" CA GLU A 342 " ideal model delta harmonic sigma weight residual 180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA GLU A 342 " pdb=" C GLU A 342 " pdb=" N LYS A 343 " pdb=" CA LYS A 343 " ideal model delta harmonic sigma weight residual 180.00 -165.15 -14.85 0 5.00e+00 4.00e-02 8.82e+00 ... (remaining 439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 54 0.057 - 0.115: 37 0.115 - 0.172: 13 0.172 - 0.230: 1 0.230 - 0.287: 2 Chirality restraints: 107 Sorted by residual: chirality pdb=" CA PRO A 270 " pdb=" N PRO A 270 " pdb=" C PRO A 270 " pdb=" CB PRO A 270 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA LEU A 357 " pdb=" N LEU A 357 " pdb=" C LEU A 357 " pdb=" CB LEU A 357 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE A 360 " pdb=" N ILE A 360 " pdb=" C ILE A 360 " pdb=" CB ILE A 360 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 104 not shown) Planarity restraints: 123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 311 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C LYS A 311 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS A 311 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO A 312 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 273 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C GLY A 273 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY A 273 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS A 274 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 378 " 0.019 2.00e-02 2.50e+03 1.26e-02 2.77e+00 pdb=" CG PHE A 378 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 378 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 378 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 378 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 378 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 378 " 0.007 2.00e-02 2.50e+03 ... (remaining 120 not shown) Histogram of nonbonded interaction distances: 2.65 - 3.10: 411 3.10 - 3.55: 539 3.55 - 4.00: 734 4.00 - 4.45: 595 4.45 - 4.90: 1174 Nonbonded interactions: 3453 Sorted by model distance: nonbonded pdb=" N ASP A 358 " pdb=" OD1 ASP A 358 " model vdw 2.651 3.120 nonbonded pdb=" N GLY A 365 " pdb=" O GLY A 365 " model vdw 2.660 2.496 nonbonded pdb=" N ASN A 368 " pdb=" O ASN A 368 " model vdw 2.680 2.496 nonbonded pdb=" O GLN A 269 " pdb=" CB GLN A 269 " model vdw 2.689 2.752 nonbonded pdb=" N ASN A 327 " pdb=" O ASN A 327 " model vdw 2.713 2.496 ... (remaining 3448 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: 2.160 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.620 Find NCS groups from input model: 0.000 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:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 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 : 0.009 0.044 722 Z= 0.603 Angle : 1.323 5.713 964 Z= 0.853 Chirality : 0.084 0.287 107 Planarity : 0.006 0.023 123 Dihedral : 11.050 47.098 280 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.78), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.60), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS A 362 PHE 0.026 0.007 PHE A 378 TYR 0.013 0.007 TYR A 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 1.1716 time to fit residues: 20.1740 Evaluate side-chains 16 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2235 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.119878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.108564 restraints weight = 831.578| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.73 r_work: 0.3419 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 722 Z= 0.117 Angle : 0.604 5.885 964 Z= 0.302 Chirality : 0.052 0.138 107 Planarity : 0.002 0.012 123 Dihedral : 4.927 15.083 95 Min Nonbonded Distance : 2.692 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.23 % Allowed : 2.47 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.80), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.002 0.001 PHE A 378 TYR 0.005 0.001 TYR A 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.091 Fit side-chains REVERT: A 372 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8168 (mt-10) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.9982 time to fit residues: 18.2140 Evaluate side-chains 19 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 overall best weight: 1.6735 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.119635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.107790 restraints weight = 863.858| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.80 r_work: 0.3411 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 722 Z= 0.132 Angle : 0.583 5.981 964 Z= 0.290 Chirality : 0.052 0.134 107 Planarity : 0.002 0.015 123 Dihedral : 4.705 15.391 95 Min Nonbonded Distance : 2.683 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.23 % Allowed : 8.64 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.80), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.003 0.001 PHE A 378 TYR 0.007 0.002 TYR A 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.083 Fit side-chains REVERT: A 372 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8207 (mt-10) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 1.0319 time to fit residues: 17.7688 Evaluate side-chains 18 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 overall best weight: 1.8735 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.119136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.107441 restraints weight = 839.891| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.79 r_work: 0.3401 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 722 Z= 0.147 Angle : 0.585 6.135 964 Z= 0.291 Chirality : 0.052 0.137 107 Planarity : 0.002 0.015 123 Dihedral : 4.679 15.833 95 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.23 % Allowed : 9.88 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.79), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.60), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.003 0.001 PHE A 378 TYR 0.007 0.002 TYR A 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.090 Fit side-chains REVERT: A 372 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8203 (mt-10) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 1.0085 time to fit residues: 18.4011 Evaluate side-chains 19 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.0020 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.121450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.109790 restraints weight = 854.925| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.79 r_work: 0.3440 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 722 Z= 0.073 Angle : 0.490 3.775 964 Z= 0.246 Chirality : 0.050 0.127 107 Planarity : 0.002 0.014 123 Dihedral : 4.298 15.115 95 Min Nonbonded Distance : 2.688 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.81), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.62), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.002 0.001 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.092 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 1.0344 time to fit residues: 18.8698 Evaluate side-chains 18 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 overall best weight: 0.9733 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.120877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.109295 restraints weight = 837.753| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.76 r_work: 0.3435 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 722 Z= 0.085 Angle : 0.500 4.309 964 Z= 0.251 Chirality : 0.050 0.130 107 Planarity : 0.002 0.013 123 Dihedral : 4.209 14.722 95 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.23 % Allowed : 9.88 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.81), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.002 0.001 PHE A 346 TYR 0.005 0.001 TYR A 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.092 Fit side-chains REVERT: A 372 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8312 (mp0) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.9855 time to fit residues: 17.9852 Evaluate side-chains 19 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.118143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106509 restraints weight = 859.535| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.80 r_work: 0.3398 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 722 Z= 0.192 Angle : 0.634 7.556 964 Z= 0.314 Chirality : 0.054 0.145 107 Planarity : 0.002 0.014 123 Dihedral : 4.589 15.953 95 Min Nonbonded Distance : 2.684 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.47 % Allowed : 8.64 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.78), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.60), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.004 0.001 PHE A 378 TYR 0.009 0.003 TYR A 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.092 Fit side-chains REVERT: A 372 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8237 (mt-10) outliers start: 2 outliers final: 0 residues processed: 17 average time/residue: 1.1159 time to fit residues: 19.2214 Evaluate side-chains 17 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.0040 chunk 8 optimal weight: 0.4980 overall best weight: 0.4995 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.122324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.110665 restraints weight = 840.507| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.75 r_work: 0.3445 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 722 Z= 0.063 Angle : 0.461 3.571 964 Z= 0.232 Chirality : 0.049 0.125 107 Planarity : 0.002 0.012 123 Dihedral : 4.181 14.899 95 Min Nonbonded Distance : 2.691 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.23 % Allowed : 11.11 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.81), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.002 0.000 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.084 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.9523 time to fit residues: 19.3079 Evaluate side-chains 17 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.0020 overall best weight: 0.9493 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.120959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.109160 restraints weight = 862.585| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.79 r_work: 0.3430 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 722 Z= 0.086 Angle : 0.492 4.152 964 Z= 0.249 Chirality : 0.050 0.129 107 Planarity : 0.002 0.013 123 Dihedral : 4.103 14.688 95 Min Nonbonded Distance : 2.696 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.80), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.002 0.001 PHE A 346 TYR 0.005 0.001 TYR A 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.081 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 1.0318 time to fit residues: 17.7696 Evaluate side-chains 17 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 1.1905 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.120363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.108627 restraints weight = 848.123| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.78 r_work: 0.3422 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 722 Z= 0.099 Angle : 0.511 4.684 964 Z= 0.258 Chirality : 0.051 0.132 107 Planarity : 0.002 0.013 123 Dihedral : 4.146 14.910 95 Min Nonbonded Distance : 2.694 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.80), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.003 0.001 PHE A 346 TYR 0.006 0.002 TYR A 310 ARG 0.000 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.093 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 1.0970 time to fit residues: 17.7924 Evaluate side-chains 16 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.0670 chunk 8 optimal weight: 2.9990 overall best weight: 1.4408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.119713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.108092 restraints weight = 839.115| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.77 r_work: 0.3421 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 722 Z= 0.116 Angle : 0.527 5.158 964 Z= 0.264 Chirality : 0.051 0.134 107 Planarity : 0.002 0.013 123 Dihedral : 4.230 15.066 95 Min Nonbonded Distance : 2.693 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.23 % Allowed : 11.11 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.79), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.003 0.001 PHE A 346 TYR 0.007 0.002 TYR A 310 ARG 0.000 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1247.10 seconds wall clock time: 22 minutes 40.63 seconds (1360.63 seconds total)