Starting phenix.real_space_refine on Wed Mar 5 21:31:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g2u_50984/03_2025/9g2u_50984.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g2u_50984/03_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_50984/03_2025/9g2u_50984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g2u_50984/03_2025/9g2u_50984.map" model { file = "/net/cci-nas-00/data/ceres_data/9g2u_50984/03_2025/9g2u_50984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g2u_50984/03_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-5624/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: 3.14, per 1000 atoms: 0.86 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: 1.00 Conformation dependent library (CDL) restraints added in 440.0 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: 0.30 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: 1.02 Time building geometry restraints manager: 1.18 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: 0.02 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.920 Find NCS groups from input model: 0.110 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- 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 : 0.470 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: 0.3416 time to fit residues: 41.0048 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 : 0.450 ------------------------------------------------------------------------------- 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: 0.9990 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 = 0.062300 restraints weight = 13983.829| |-----------------------------------------------------------------------------| 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 : 0.463 Fit side-chains REVERT: A 26 THR cc_start: 0.9288 (m) cc_final: 0.9079 (p) REVERT: A 101 MET cc_start: 0.8852 (mtt) cc_final: 0.8534 (mtm) REVERT: A 171 ASP cc_start: 0.8209 (m-30) cc_final: 0.7711 (m-30) REVERT: B 26 THR cc_start: 0.9288 (m) cc_final: 0.9037 (p) REVERT: B 188 ARG cc_start: 0.6805 (ttt90) cc_final: 0.6102 (mtm-85) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.1622 time to fit residues: 12.8895 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 : 0.447 ------------------------------------------------------------------------------- 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: 0.8980 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.0030 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.075839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.061137 restraints weight = 14127.769| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.67 r_work: 0.3186 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5301 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= 0.185 Angle : 0.505 6.960 4952 Z= 0.279 Chirality : 0.032 0.130 564 Planarity : 0.003 0.026 644 Dihedral : 2.787 17.645 492 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 2.84 % Allowed : 9.79 % 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: 6.19 (0.34), residues: 448 helix: 4.31 (0.21), residues: 420 sheet: None (None), residues: 0 loop : -1.75 (0.81), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 55 HIS 0.002 0.001 HIS B 220 PHE 0.017 0.001 PHE A 18 TYR 0.016 0.001 TYR A 155 ARG 0.005 0.001 ARG B 162 *********************** 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 57 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.479 Fit side-chains REVERT: A 26 THR cc_start: 0.9316 (m) cc_final: 0.9109 (p) REVERT: A 101 MET cc_start: 0.8856 (mtt) cc_final: 0.8503 (mtm) REVERT: B 103 ASP cc_start: 0.9091 (m-30) cc_final: 0.8695 (m-30) REVERT: B 134 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8826 (tm-30) REVERT: B 232 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8358 (tm-30) REVERT: B 235 MET cc_start: 0.9130 (tmm) cc_final: 0.8448 (tmm) outliers start: 11 outliers final: 5 residues processed: 53 average time/residue: 0.1548 time to fit residues: 10.3412 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 : 0.411 ------------------------------------------------------------------------------- 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 51 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 GLN ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.072625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.058313 restraints weight = 14433.975| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.66 r_work: 0.3116 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5771 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= 0.233 Angle : 0.542 9.983 4952 Z= 0.291 Chirality : 0.033 0.121 564 Planarity : 0.003 0.025 644 Dihedral : 2.822 14.312 492 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.84 % Allowed : 9.79 % 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: 5.93 (0.34), residues: 448 helix: 4.13 (0.21), residues: 420 sheet: None (None), residues: 0 loop : -1.56 (0.85), 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 0.018 0.002 PHE B 18 TYR 0.016 0.002 TYR A 155 ARG 0.013 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 56 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.9334 (m) cc_final: 0.9128 (p) REVERT: A 101 MET cc_start: 0.8860 (mtt) cc_final: 0.8496 (mtm) REVERT: A 195 LEU cc_start: 0.9098 (tp) cc_final: 0.8626 (mm) REVERT: B 103 ASP cc_start: 0.9162 (m-30) cc_final: 0.8787 (m-30) REVERT: B 188 ARG cc_start: 0.7288 (ttt90) cc_final: 0.6570 (mtm-85) REVERT: B 232 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8460 (tm-30) REVERT: B 235 MET cc_start: 0.9102 (tmm) cc_final: 0.8432 (tmm) outliers start: 11 outliers final: 10 residues processed: 52 average time/residue: 0.1189 time to fit residues: 8.3151 Evaluate side-chains 49 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET 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 Chi-restraints excluded: chain B residue 199 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 243 GLN B 234 GLN B 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.071970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.057675 restraints weight = 14735.010| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.73 r_work: 0.3096 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3680 Z= 0.251 Angle : 0.543 8.778 4952 Z= 0.292 Chirality : 0.033 0.120 564 Planarity : 0.003 0.032 644 Dihedral : 2.826 12.674 492 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.58 % Allowed : 11.60 % 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: 5.87 (0.34), residues: 448 helix: 4.10 (0.21), residues: 420 sheet: None (None), residues: 0 loop : -1.57 (0.90), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 55 HIS 0.002 0.000 HIS B 222 PHE 0.014 0.002 PHE B 143 TYR 0.016 0.002 TYR A 155 ARG 0.004 0.001 ARG A 21 *********************** 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 51 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.463 Fit side-chains REVERT: A 26 THR cc_start: 0.9336 (m) cc_final: 0.9121 (p) REVERT: B 103 ASP cc_start: 0.9176 (m-30) cc_final: 0.8821 (m-30) REVERT: B 134 GLU cc_start: 0.9175 (tt0) cc_final: 0.8934 (tm-30) REVERT: B 232 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8518 (tm-30) REVERT: B 235 MET cc_start: 0.9138 (tmm) cc_final: 0.8429 (tmm) outliers start: 10 outliers final: 8 residues processed: 48 average time/residue: 0.1186 time to fit residues: 8.0100 Evaluate side-chains 46 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET 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 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: 0.6980 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.073196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.058879 restraints weight = 14771.262| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.75 r_work: 0.3129 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.6608 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= 0.191 Angle : 0.509 8.368 4952 Z= 0.268 Chirality : 0.031 0.121 564 Planarity : 0.003 0.028 644 Dihedral : 2.756 11.485 492 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 2.32 % Allowed : 11.86 % 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: 6.14 (0.35), residues: 448 helix: 4.28 (0.21), residues: 420 sheet: None (None), residues: 0 loop : -1.58 (0.91), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 55 HIS 0.002 0.000 HIS B 220 PHE 0.019 0.002 PHE B 18 TYR 0.016 0.001 TYR A 155 ARG 0.003 0.001 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 51 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.480 Fit side-chains REVERT: A 26 THR cc_start: 0.9313 (m) cc_final: 0.9092 (p) REVERT: B 103 ASP cc_start: 0.9162 (m-30) cc_final: 0.8813 (m-30) REVERT: B 188 ARG cc_start: 0.7411 (ttt90) cc_final: 0.6812 (ttm-80) REVERT: B 232 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8617 (tm-30) REVERT: B 235 MET cc_start: 0.9231 (tmm) cc_final: 0.8454 (tmm) outliers start: 9 outliers final: 5 residues processed: 48 average time/residue: 0.1070 time to fit residues: 7.2946 Evaluate side-chains 43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 2 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: 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 = 0.073238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.058680 restraints weight = 14532.733| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.77 r_work: 0.3128 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.6840 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= 0.193 Angle : 0.501 7.865 4952 Z= 0.265 Chirality : 0.032 0.143 564 Planarity : 0.003 0.026 644 Dihedral : 2.742 11.808 492 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 2.06 % Allowed : 13.14 % Favored : 84.79 % 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 (0.35), residues: 448 helix: 4.28 (0.21), residues: 420 sheet: None (None), residues: 0 loop : -1.64 (0.93), 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 0.020 0.002 PHE B 25 TYR 0.016 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 48 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.403 Fit side-chains REVERT: A 26 THR cc_start: 0.9292 (m) cc_final: 0.9079 (p) REVERT: A 249 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8523 (tt0) REVERT: B 103 ASP cc_start: 0.9173 (m-30) cc_final: 0.8823 (m-30) REVERT: B 188 ARG cc_start: 0.7534 (ttt90) cc_final: 0.6870 (ttm-80) REVERT: B 232 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8669 (tm-30) REVERT: B 235 MET cc_start: 0.9253 (tmm) cc_final: 0.8552 (tmm) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.1073 time to fit residues: 6.9053 Evaluate side-chains 44 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 60 MET Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.073517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058948 restraints weight = 14306.334| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.77 r_work: 0.3137 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3680 Z= 0.203 Angle : 0.505 7.461 4952 Z= 0.268 Chirality : 0.032 0.134 564 Planarity : 0.003 0.023 644 Dihedral : 2.789 11.971 492 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.06 % Allowed : 13.66 % Favored : 84.28 % 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: 6.02 (0.35), residues: 448 helix: 4.20 (0.21), residues: 420 sheet: None (None), residues: 0 loop : -1.62 (0.94), residues: 28 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 55 HIS 0.001 0.000 HIS B 222 PHE 0.021 0.003 PHE B 18 TYR 0.016 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 46 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.422 Fit side-chains REVERT: A 26 THR cc_start: 0.9289 (m) cc_final: 0.9065 (p) REVERT: B 103 ASP cc_start: 0.9175 (m-30) cc_final: 0.8823 (m-30) REVERT: B 173 ASP cc_start: 0.8556 (m-30) cc_final: 0.8195 (t0) REVERT: B 188 ARG cc_start: 0.7644 (ttt90) cc_final: 0.7326 (mtt-85) REVERT: B 232 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8615 (tm-30) REVERT: B 235 MET cc_start: 0.9288 (tmm) cc_final: 0.8519 (tmm) outliers start: 8 outliers final: 7 residues processed: 43 average time/residue: 0.1119 time to fit residues: 6.6707 Evaluate side-chains 42 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 60 MET Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.073914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.059318 restraints weight = 14341.755| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.81 r_work: 0.3151 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.7078 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= 0.181 Angle : 0.497 7.472 4952 Z= 0.265 Chirality : 0.032 0.128 564 Planarity : 0.003 0.023 644 Dihedral : 2.757 12.009 492 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 2.06 % Allowed : 12.63 % Favored : 85.31 % 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: 6.19 (0.35), residues: 448 helix: 4.25 (0.22), residues: 424 sheet: None (None), residues: 0 loop : -1.53 (1.03), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 55 HIS 0.001 0.000 HIS B 222 PHE 0.018 0.002 PHE B 25 TYR 0.015 0.001 TYR A 155 ARG 0.003 0.000 ARG B 178 *********************** 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 45 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.453 Fit side-chains REVERT: A 26 THR cc_start: 0.9283 (m) cc_final: 0.9058 (p) REVERT: A 171 ASP cc_start: 0.8231 (m-30) cc_final: 0.7967 (m-30) REVERT: B 64 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: B 103 ASP cc_start: 0.9163 (m-30) cc_final: 0.8810 (m-30) REVERT: B 171 ASP cc_start: 0.9194 (p0) cc_final: 0.8877 (m-30) REVERT: B 188 ARG cc_start: 0.7696 (ttt90) cc_final: 0.7140 (ttm-80) REVERT: B 232 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8619 (tm-30) REVERT: B 235 MET cc_start: 0.9270 (tmm) cc_final: 0.8500 (tmm) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.1123 time to fit residues: 6.6193 Evaluate side-chains 43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 231 VAL Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 64 GLU 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 27 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 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 = 0.3630 r_free = 0.3630 target = 0.073823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.059087 restraints weight = 14498.167| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.83 r_work: 0.3143 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.7120 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= 0.189 Angle : 0.506 8.551 4952 Z= 0.268 Chirality : 0.032 0.122 564 Planarity : 0.003 0.023 644 Dihedral : 2.750 11.965 492 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 2.06 % Allowed : 12.63 % Favored : 85.31 % 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: 6.21 (0.35), residues: 448 helix: 4.27 (0.22), residues: 424 sheet: None (None), residues: 0 loop : -1.56 (1.02), 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 0.022 0.002 PHE B 18 TYR 0.015 0.001 TYR A 155 ARG 0.003 0.000 ARG A 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 45 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.453 Fit side-chains REVERT: A 26 THR cc_start: 0.9291 (m) cc_final: 0.9067 (p) REVERT: A 171 ASP cc_start: 0.8269 (m-30) cc_final: 0.8008 (m-30) REVERT: B 64 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8319 (pt0) REVERT: B 103 ASP cc_start: 0.9195 (m-30) cc_final: 0.8853 (m-30) REVERT: B 171 ASP cc_start: 0.9211 (p0) cc_final: 0.8872 (m-30) REVERT: B 188 ARG cc_start: 0.7930 (ttt90) cc_final: 0.7548 (ttm-80) REVERT: B 232 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8629 (tm-30) REVERT: B 235 MET cc_start: 0.9255 (tmm) cc_final: 0.8482 (tmm) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.1129 time to fit residues: 6.6434 Evaluate side-chains 43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 231 VAL Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 64 GLU 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: 2.9990 chunk 17 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.074157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.059411 restraints weight = 14399.706| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.83 r_work: 0.3154 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.7232 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= 0.187 Angle : 0.496 7.311 4952 Z= 0.264 Chirality : 0.031 0.124 564 Planarity : 0.003 0.023 644 Dihedral : 2.740 11.966 492 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.55 % Allowed : 13.40 % Favored : 85.05 % 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: 6.28 (0.35), residues: 448 helix: 4.31 (0.21), residues: 424 sheet: None (None), residues: 0 loop : -1.58 (1.01), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 55 HIS 0.001 0.000 HIS B 222 PHE 0.011 0.001 PHE B 143 TYR 0.015 0.001 TYR A 155 ARG 0.002 0.000 ARG A 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2135.23 seconds wall clock time: 37 minutes 16.93 seconds (2236.93 seconds total)