Starting phenix.real_space_refine on Tue Feb 11 02:19:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g2u_50984/02_2025/9g2u_50984.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g2u_50984/02_2025/9g2u_50984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g2u_50984/02_2025/9g2u_50984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g2u_50984/02_2025/9g2u_50984.map" model { file = "/net/cci-nas-00/data/ceres_data/9g2u_50984/02_2025/9g2u_50984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g2u_50984/02_2025/9g2u_50984.cif" } resolution = 3.45 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= 0.018 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 16 5.16 5 C 2272 2.51 5 N 640 2.21 5 O 706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3634 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1817 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1817 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Time building chain proxies: 2.82, per 1000 atoms: 0.78 Number of scatterers: 3634 At special positions: 0 Unit cell: (100.928, 83.664, 131.472, 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 16 16.00 O 706 8.00 N 640 7.00 C 2272 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: 0.83 Conformation dependent library (CDL) restraints added in 430.9 milliseconds 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 868 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 95.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 11 through 31 removed outlier: 3.851A pdb=" N ALA A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 68 Processing helix chain 'A' and resid 70 through 76 Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 112 through 143 Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.688A pdb=" N ILE A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 181 Processing helix chain 'A' and resid 184 through 252 removed outlier: 3.864A pdb=" N ILE A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 31 Processing helix chain 'B' and resid 39 through 68 Processing helix chain 'B' and resid 70 through 76 Processing helix chain 'B' and resid 92 through 109 Processing helix chain 'B' and resid 112 through 143 Processing helix chain 'B' and resid 143 through 153 Processing helix chain 'B' and resid 153 through 182 Processing helix chain 'B' and resid 184 through 252 removed outlier: 3.820A pdb=" N ILE B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 1077 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: 1.05 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 787 1.33 - 1.45: 731 1.45 - 1.57: 2138 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3680 Sorted by residual: bond pdb=" N THR A 145 " pdb=" CA THR A 145 " ideal model delta sigma weight residual 1.462 1.488 -0.026 7.70e-03 1.69e+04 1.15e+01 bond pdb=" N ASN B 93 " pdb=" CA ASN B 93 " ideal model delta sigma weight residual 1.461 1.488 -0.027 9.20e-03 1.18e+04 8.53e+00 bond pdb=" N LEU B 38 " pdb=" CA LEU B 38 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.16e-02 7.43e+03 8.29e+00 bond pdb=" N ILE A 216 " pdb=" CA ILE A 216 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.24e-02 6.50e+03 8.03e+00 bond pdb=" N GLU B 37 " pdb=" CA GLU B 37 " ideal model delta sigma weight residual 1.453 1.488 -0.034 1.22e-02 6.72e+03 7.97e+00 ... (remaining 3675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 2935 1.00 - 2.00: 894 2.00 - 3.00: 1074 3.00 - 4.00: 40 4.00 - 5.00: 9 Bond angle restraints: 4952 Sorted by residual: angle pdb=" N GLN A 32 " pdb=" CA GLN A 32 " pdb=" C GLN A 32 " ideal model delta sigma weight residual 113.20 108.89 4.31 1.21e+00 6.83e-01 1.27e+01 angle pdb=" N GLY B 31 " pdb=" CA GLY B 31 " pdb=" C GLY B 31 " ideal model delta sigma weight residual 115.21 110.77 4.44 1.30e+00 5.92e-01 1.17e+01 angle pdb=" CA ALA B 182 " pdb=" C ALA B 182 " pdb=" O ALA B 182 " ideal model delta sigma weight residual 122.41 118.33 4.08 1.21e+00 6.83e-01 1.14e+01 angle pdb=" N GLY A 31 " pdb=" CA GLY A 31 " pdb=" C GLY A 31 " ideal model delta sigma weight residual 115.21 110.86 4.35 1.30e+00 5.92e-01 1.12e+01 angle pdb=" N LYS A 183 " pdb=" CA LYS A 183 " pdb=" C LYS A 183 " ideal model delta sigma weight residual 114.39 109.58 4.81 1.45e+00 4.76e-01 1.10e+01 ... (remaining 4947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 2100 15.96 - 31.92: 142 31.92 - 47.88: 13 47.88 - 63.85: 26 63.85 - 79.81: 1 Dihedral angle restraints: 2282 sinusoidal: 948 harmonic: 1334 Sorted by residual: dihedral pdb=" CD ARG A 225 " pdb=" NE ARG A 225 " pdb=" CZ ARG A 225 " pdb=" NH1 ARG A 225 " ideal model delta sinusoidal sigma weight residual 0.00 -30.30 30.30 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CD ARG B 225 " pdb=" NE ARG B 225 " pdb=" CZ ARG B 225 " pdb=" NH1 ARG B 225 " ideal model delta sinusoidal sigma weight residual 0.00 -26.50 26.50 1 1.00e+01 1.00e-02 1.01e+01 dihedral pdb=" CB MET A 245 " pdb=" CG MET A 245 " pdb=" SD MET A 245 " pdb=" CE MET A 245 " ideal model delta sinusoidal sigma weight residual 60.00 112.23 -52.23 3 1.50e+01 4.44e-03 9.09e+00 ... (remaining 2279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 128 0.044 - 0.088: 161 0.088 - 0.132: 161 0.132 - 0.176: 94 0.176 - 0.220: 20 Chirality restraints: 564 Sorted by residual: chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE A 208 " pdb=" N ILE A 208 " pdb=" C ILE A 208 " pdb=" CB ILE A 208 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE B 75 " pdb=" N ILE B 75 " pdb=" C ILE B 75 " pdb=" CB ILE B 75 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 561 not shown) Planarity restraints: 644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 225 " 0.542 9.50e-02 1.11e+02 2.43e-01 3.61e+01 pdb=" NE ARG A 225 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 225 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 225 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 225 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 225 " 0.478 9.50e-02 1.11e+02 2.14e-01 2.81e+01 pdb=" NE ARG B 225 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 225 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 225 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 225 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 204 " -0.378 9.50e-02 1.11e+02 1.69e-01 1.76e+01 pdb=" NE ARG B 204 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 204 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 204 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 204 " -0.012 2.00e-02 2.50e+03 ... (remaining 641 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 59 2.68 - 3.24: 3938 3.24 - 3.79: 6011 3.79 - 4.35: 7726 4.35 - 4.90: 12141 Nonbonded interactions: 29875 Sorted by model distance: nonbonded pdb=" NE1 TRP A 55 " pdb=" OE1 GLU B 107 " model vdw 2.127 3.120 nonbonded pdb=" CB CYS A 51 " pdb=" OE2 GLU B 107 " model vdw 2.208 3.440 nonbonded pdb=" CD1 PHE B 150 " pdb=" CG2 THR B 219 " model vdw 2.370 3.760 nonbonded pdb=" SG CYS A 51 " pdb=" OE2 GLU B 107 " model vdw 2.375 3.400 nonbonded pdb=" ND1 HIS A 222 " pdb=" NH2 ARG A 225 " model vdw 2.431 3.200 ... (remaining 29870 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.860 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 : 0.011 0.036 3680 Z= 0.742 Angle : 1.371 4.996 4952 Z= 1.172 Chirality : 0.101 0.220 564 Planarity : 0.021 0.243 644 Dihedral : 12.819 79.808 1414 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.26 % Allowed : 1.55 % Favored : 98.20 % 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: 1.40 (0.32), residues: 448 helix: 1.26 (0.20), residues: 414 sheet: None (None), residues: 0 loop : -2.64 (0.68), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 55 HIS 0.003 0.001 HIS A 222 PHE 0.006 0.001 PHE B 150 TYR 0.005 0.001 TYR A 244 ARG 0.004 0.001 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.9197 (tp) cc_final: 0.8711 (tt) REVERT: A 101 MET cc_start: 0.8470 (mtt) cc_final: 0.8121 (mtt) REVERT: A 190 SER cc_start: 0.8445 (t) cc_final: 0.7725 (p) REVERT: A 216 ILE cc_start: 0.9283 (mm) cc_final: 0.8862 (tt) REVERT: B 46 LEU cc_start: 0.9394 (mt) cc_final: 0.9119 (mt) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.3205 time to fit residues: 38.4569 Evaluate side-chains 54 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 251 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.076641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.062299 restraints weight = 13983.814| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.39 r_work: 0.3244 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3680 Z= 0.232 Angle : 0.586 5.465 4952 Z= 0.323 Chirality : 0.035 0.122 564 Planarity : 0.005 0.040 644 Dihedral : 2.871 15.478 492 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.55 % Allowed : 8.25 % Favored : 90.21 % 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: 5.30 (0.34), residues: 448 helix: 3.73 (0.21), residues: 420 sheet: None (None), residues: 0 loop : -1.66 (0.77), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 55 HIS 0.002 0.001 HIS B 220 PHE 0.012 0.002 PHE A 143 TYR 0.015 0.001 TYR A 155 ARG 0.007 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.419 Fit side-chains REVERT: A 26 THR cc_start: 0.9288 (m) cc_final: 0.9079 (p) REVERT: A 101 MET cc_start: 0.8851 (mtt) cc_final: 0.8534 (mtm) REVERT: A 171 ASP cc_start: 0.8210 (m-30) cc_final: 0.7712 (m-30) REVERT: B 26 THR cc_start: 0.9288 (m) cc_final: 0.9037 (p) REVERT: B 188 ARG cc_start: 0.6804 (ttt90) cc_final: 0.6101 (mtm-85) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.1588 time to fit residues: 12.5230 Evaluate side-chains 45 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 64 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.0050 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.075397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.060722 restraints weight = 14157.106| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.66 r_work: 0.3179 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3680 Z= 0.186 Angle : 0.505 6.227 4952 Z= 0.280 Chirality : 0.032 0.116 564 Planarity : 0.003 0.026 644 Dihedral : 2.813 17.833 492 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 3.09 % Allowed : 9.54 % Favored : 87.37 % 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: 6.14 (0.34), residues: 448 helix: 4.28 (0.21), residues: 420 sheet: None (None), residues: 0 loop : -1.72 (0.83), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 55 HIS 0.002 0.001 HIS B 220 PHE 0.018 0.002 PHE A 18 TYR 0.016 0.001 TYR A 155 ARG 0.006 0.001 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.9322 (m) cc_final: 0.9115 (p) REVERT: A 101 MET cc_start: 0.8858 (mtt) cc_final: 0.8514 (mtm) REVERT: B 103 ASP cc_start: 0.9096 (m-30) cc_final: 0.8697 (m-30) REVERT: B 134 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8836 (tm-30) REVERT: B 232 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8444 (tm-30) REVERT: B 235 MET cc_start: 0.9103 (tmm) cc_final: 0.8433 (tmm) outliers start: 12 outliers final: 7 residues processed: 55 average time/residue: 0.1506 time to fit residues: 10.4680 Evaluate side-chains 47 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 199 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.074015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.059659 restraints weight = 14440.541| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.67 r_work: 0.3150 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3680 Z= 0.194 Angle : 0.492 5.911 4952 Z= 0.269 Chirality : 0.032 0.122 564 Planarity : 0.003 0.024 644 Dihedral : 2.783 13.981 492 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 2.84 % Allowed : 9.28 % Favored : 87.89 % 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: 6.10 (0.34), residues: 448 helix: 4.25 (0.21), residues: 420 sheet: None (None), residues: 0 loop : -1.63 (0.84), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 55 HIS 0.003 0.001 HIS A 41 PHE 0.020 0.002 PHE B 18 TYR 0.017 0.001 TYR A 155 ARG 0.010 0.001 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.455 Fit side-chains REVERT: A 26 THR cc_start: 0.9320 (m) cc_final: 0.9116 (p) REVERT: A 101 MET cc_start: 0.8881 (mtt) cc_final: 0.8526 (mtm) REVERT: A 195 LEU cc_start: 0.9082 (tp) cc_final: 0.8601 (mm) REVERT: B 60 MET cc_start: 0.8928 (ttm) cc_final: 0.8678 (ttm) REVERT: B 103 ASP cc_start: 0.9159 (m-30) cc_final: 0.8794 (m-30) REVERT: B 188 ARG cc_start: 0.7209 (ttt90) cc_final: 0.6524 (mtm-85) REVERT: B 232 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8457 (tm-30) REVERT: B 235 MET cc_start: 0.9084 (tmm) cc_final: 0.8410 (tmm) outliers start: 11 outliers final: 8 residues processed: 48 average time/residue: 0.1067 time to fit residues: 7.1270 Evaluate side-chains 44 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 205 GLN B 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.073413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.058990 restraints weight = 14690.507| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.77 r_work: 0.3127 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3680 Z= 0.193 Angle : 0.489 9.679 4952 Z= 0.260 Chirality : 0.031 0.125 564 Planarity : 0.003 0.031 644 Dihedral : 2.709 12.139 492 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.58 % Allowed : 10.82 % Favored : 86.60 % 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: 6.13 (0.34), residues: 448 helix: 4.27 (0.21), residues: 420 sheet: None (None), residues: 0 loop : -1.57 (0.89), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 55 HIS 0.001 0.000 HIS B 220 PHE 0.019 0.002 PHE B 25 TYR 0.016 0.001 TYR A 155 ARG 0.004 0.001 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 26 THR cc_start: 0.9292 (m) cc_final: 0.9070 (p) REVERT: A 101 MET cc_start: 0.8854 (mtt) cc_final: 0.8513 (mtm) REVERT: B 60 MET cc_start: 0.8909 (ttm) cc_final: 0.8663 (ttm) REVERT: B 103 ASP cc_start: 0.9186 (m-30) cc_final: 0.8827 (m-30) REVERT: B 134 GLU cc_start: 0.9144 (tt0) cc_final: 0.8895 (tm-30) REVERT: B 188 ARG cc_start: 0.7360 (ttt90) cc_final: 0.6634 (mtm-85) REVERT: B 232 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8533 (tm-30) REVERT: B 235 MET cc_start: 0.9141 (tmm) cc_final: 0.8524 (tmm) outliers start: 10 outliers final: 6 residues processed: 51 average time/residue: 0.1073 time to fit residues: 7.5523 Evaluate side-chains 43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.073895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.059303 restraints weight = 14716.171| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.82 r_work: 0.3138 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3680 Z= 0.189 Angle : 0.509 9.140 4952 Z= 0.269 Chirality : 0.032 0.156 564 Planarity : 0.003 0.026 644 Dihedral : 2.708 11.194 492 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.80 % Allowed : 11.60 % Favored : 86.60 % 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: 6.15 (0.34), residues: 448 helix: 4.28 (0.21), residues: 420 sheet: None (None), residues: 0 loop : -1.50 (0.92), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 55 HIS 0.001 0.000 HIS B 222 PHE 0.019 0.002 PHE B 18 TYR 0.016 0.001 TYR A 155 ARG 0.003 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.450 Fit side-chains REVERT: A 26 THR cc_start: 0.9303 (m) cc_final: 0.9079 (p) REVERT: A 101 MET cc_start: 0.8858 (mtt) cc_final: 0.8509 (mtm) REVERT: B 103 ASP cc_start: 0.9183 (m-30) cc_final: 0.8831 (m-30) REVERT: B 134 GLU cc_start: 0.9114 (tt0) cc_final: 0.8912 (tm-30) REVERT: B 178 ARG cc_start: 0.8960 (mtp-110) cc_final: 0.8409 (ttp-170) REVERT: B 188 ARG cc_start: 0.7362 (ttt90) cc_final: 0.6713 (mtm-85) REVERT: B 232 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8612 (tm-30) REVERT: B 235 MET cc_start: 0.9149 (tmm) cc_final: 0.8529 (tmm) outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.1343 time to fit residues: 8.0418 Evaluate side-chains 43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.073177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.058744 restraints weight = 14540.373| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.77 r_work: 0.3129 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.6721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3680 Z= 0.196 Angle : 0.494 8.451 4952 Z= 0.263 Chirality : 0.031 0.120 564 Planarity : 0.003 0.024 644 Dihedral : 2.713 11.694 492 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.80 % Allowed : 12.37 % Favored : 85.82 % 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: 6.09 (0.34), residues: 448 helix: 4.24 (0.21), residues: 420 sheet: None (None), residues: 0 loop : -1.46 (0.95), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 55 HIS 0.001 0.000 HIS B 222 PHE 0.013 0.001 PHE B 143 TYR 0.015 0.001 TYR A 155 ARG 0.003 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.421 Fit side-chains REVERT: A 26 THR cc_start: 0.9277 (m) cc_final: 0.9050 (p) REVERT: A 101 MET cc_start: 0.8852 (mtt) cc_final: 0.8509 (mtm) REVERT: A 249 GLN cc_start: 0.8911 (tm-30) cc_final: 0.8641 (tt0) REVERT: B 103 ASP cc_start: 0.9186 (m-30) cc_final: 0.8836 (m-30) REVERT: B 232 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8669 (tm-30) REVERT: B 235 MET cc_start: 0.9236 (tmm) cc_final: 0.8723 (tmm) outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 0.1206 time to fit residues: 7.1346 Evaluate side-chains 42 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 51 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.074684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.060149 restraints weight = 14415.234| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.75 r_work: 0.3170 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.6905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3680 Z= 0.175 Angle : 0.493 8.047 4952 Z= 0.257 Chirality : 0.031 0.120 564 Planarity : 0.003 0.022 644 Dihedral : 2.694 11.700 492 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.55 % Allowed : 11.86 % Favored : 86.60 % 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: 6.25 (0.35), residues: 448 helix: 4.29 (0.21), residues: 424 sheet: None (None), residues: 0 loop : -1.38 (1.06), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 55 HIS 0.001 0.000 HIS B 222 PHE 0.021 0.002 PHE B 18 TYR 0.015 0.001 TYR A 155 ARG 0.003 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 26 THR cc_start: 0.9258 (m) cc_final: 0.9028 (p) REVERT: A 101 MET cc_start: 0.8834 (mtt) cc_final: 0.8493 (mtm) REVERT: A 249 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8635 (tt0) REVERT: B 103 ASP cc_start: 0.9175 (m-30) cc_final: 0.8819 (m-30) REVERT: B 188 ARG cc_start: 0.7519 (ttt90) cc_final: 0.6904 (ttm-80) REVERT: B 232 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8700 (tm-30) REVERT: B 235 MET cc_start: 0.9225 (tmm) cc_final: 0.8521 (tmm) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 0.1178 time to fit residues: 7.0324 Evaluate side-chains 40 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 51 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.073842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.059160 restraints weight = 14368.711| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.77 r_work: 0.3147 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3680 Z= 0.197 Angle : 0.508 8.109 4952 Z= 0.267 Chirality : 0.031 0.120 564 Planarity : 0.003 0.022 644 Dihedral : 2.708 12.007 492 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.80 % Allowed : 12.11 % Favored : 86.08 % 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: 6.18 (0.35), residues: 448 helix: 4.24 (0.21), residues: 424 sheet: None (None), residues: 0 loop : -1.42 (1.06), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 55 HIS 0.001 0.000 HIS B 222 PHE 0.019 0.002 PHE B 25 TYR 0.015 0.001 TYR A 155 ARG 0.003 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 26 THR cc_start: 0.9274 (m) cc_final: 0.9047 (p) REVERT: A 101 MET cc_start: 0.8752 (mtt) cc_final: 0.8449 (mtm) REVERT: A 171 ASP cc_start: 0.8249 (m-30) cc_final: 0.7988 (m-30) REVERT: B 103 ASP cc_start: 0.9187 (m-30) cc_final: 0.8840 (m-30) REVERT: B 188 ARG cc_start: 0.7594 (ttt90) cc_final: 0.6967 (ttm-80) REVERT: B 232 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8709 (tm-30) REVERT: B 235 MET cc_start: 0.9228 (tmm) cc_final: 0.8555 (tmm) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 0.1172 time to fit residues: 7.2141 Evaluate side-chains 41 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 60 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.073193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.058553 restraints weight = 14576.213| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.81 r_work: 0.3128 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.6979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3680 Z= 0.219 Angle : 0.523 8.247 4952 Z= 0.277 Chirality : 0.032 0.124 564 Planarity : 0.003 0.022 644 Dihedral : 2.762 12.140 492 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.80 % Allowed : 12.63 % Favored : 85.57 % 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: 6.10 (0.34), residues: 448 helix: 4.19 (0.21), residues: 424 sheet: None (None), residues: 0 loop : -1.41 (1.06), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 55 HIS 0.002 0.001 HIS A 220 PHE 0.025 0.002 PHE A 18 TYR 0.015 0.001 TYR A 155 ARG 0.003 0.000 ARG B 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 26 THR cc_start: 0.9274 (m) cc_final: 0.9051 (p) REVERT: A 171 ASP cc_start: 0.8368 (m-30) cc_final: 0.8119 (m-30) REVERT: B 103 ASP cc_start: 0.9195 (m-30) cc_final: 0.8851 (m-30) REVERT: B 173 ASP cc_start: 0.8608 (m-30) cc_final: 0.8228 (t0) REVERT: B 188 ARG cc_start: 0.7811 (ttt90) cc_final: 0.7446 (ttm-80) REVERT: B 232 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8665 (tm-30) REVERT: B 235 MET cc_start: 0.9318 (tmm) cc_final: 0.8506 (tmm) outliers start: 7 outliers final: 6 residues processed: 42 average time/residue: 0.1252 time to fit residues: 7.2621 Evaluate side-chains 41 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.0060 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.074698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.060093 restraints weight = 14486.312| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.86 r_work: 0.3170 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.7208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3680 Z= 0.174 Angle : 0.492 8.036 4952 Z= 0.258 Chirality : 0.031 0.119 564 Planarity : 0.003 0.022 644 Dihedral : 2.693 12.291 492 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.55 % Allowed : 12.63 % Favored : 85.82 % 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: 6.39 (0.35), residues: 448 helix: 4.38 (0.22), residues: 424 sheet: None (None), residues: 0 loop : -1.43 (1.08), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 55 HIS 0.001 0.000 HIS A 220 PHE 0.025 0.002 PHE A 18 TYR 0.015 0.001 TYR B 155 ARG 0.003 0.000 ARG B 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.10 seconds wall clock time: 37 minutes 42.32 seconds (2262.32 seconds total)