Starting phenix.real_space_refine on Fri May 16 03:55:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmb_27533/05_2025/8dmb_27533.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmb_27533/05_2025/8dmb_27533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dmb_27533/05_2025/8dmb_27533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmb_27533/05_2025/8dmb_27533.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmb_27533/05_2025/8dmb_27533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmb_27533/05_2025/8dmb_27533.cif" } resolution = 3.1 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= 0.006 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: 7 Type Number sf(0) Gaussians P 274 5.49 5 Mg 2 5.21 5 S 9 5.16 5 C 4303 2.51 5 N 1586 2.21 5 O 2323 1.98 5 H 5728 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14225 Number of models: 1 Model: "" Number of chains: 5 Chain: "P" Number of atoms: 5376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5376 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 20, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "W" Number of atoms: 7634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 7634 Classifications: {'RNA': 237} Modifications used: {'3*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 14, 'rna3p_pur': 109, 'rna3p_pyr': 103} Link IDs: {'rna2p': 25, 'rna3p': 211} Chain breaks: 4 Chain: "X" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 893 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "Y" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 320 Classifications: {'DNA': 10} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 9} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.86, per 1000 atoms: 0.48 Number of scatterers: 14225 At special positions: 0 Unit cell: (108.68, 128.128, 102.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 9 16.00 P 274 15.00 Mg 2 11.99 O 2323 8.00 N 1586 7.00 C 4303 6.00 H 5728 1.00 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: 3.45 Conformation dependent library (CDL) restraints added in 591.1 milliseconds 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 604 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 3 sheets defined 34.5% alpha, 21.3% beta 108 base pairs and 159 stacking pairs defined. Time for finding SS restraints: 7.41 Creating SS restraints... Processing helix chain 'P' and resid 22 through 32 Processing helix chain 'P' and resid 92 through 112 Processing helix chain 'P' and resid 130 through 151 removed outlier: 4.105A pdb=" N ILE P 150 " --> pdb=" O GLU P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 168 Processing helix chain 'P' and resid 171 through 179 removed outlier: 4.974A pdb=" N VAL P 177 " --> pdb=" O TYR P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 192 removed outlier: 3.668A pdb=" N LYS P 190 " --> pdb=" O ARG P 186 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU P 191 " --> pdb=" O GLU P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 210 Processing helix chain 'P' and resid 226 through 239 Processing helix chain 'P' and resid 267 through 271 removed outlier: 3.581A pdb=" N VAL P 271 " --> pdb=" O LYS P 268 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 10 through 11 removed outlier: 7.201A pdb=" N VAL P 11 " --> pdb=" O MET P 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 193 through 197 removed outlier: 3.640A pdb=" N LEU P 155 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU P 159 " --> pdb=" O VAL P 64 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER P 77 " --> pdb=" O VAL P 81 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL P 81 " --> pdb=" O SER P 77 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N PHE P 249 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG P 84 " --> pdb=" O PHE P 249 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N TRP P 251 " --> pdb=" O ARG P 84 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N MET P 86 " --> pdb=" O TRP P 251 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ARG P 253 " --> pdb=" O MET P 86 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE P 88 " --> pdb=" O ARG P 253 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE P 248 " --> pdb=" O VAL P 346 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG P 252 " --> pdb=" O SER P 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 323 through 327 removed outlier: 6.074A pdb=" N GLY P 315 " --> pdb=" O CYS P 304 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU P 291 " --> pdb=" O LEU P 334 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU P 334 " --> pdb=" O GLU P 291 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU P 293 " --> pdb=" O VAL P 332 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL P 332 " --> pdb=" O GLU P 293 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 330 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 285 hydrogen bonds 526 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 159 stacking parallelities Total time for adding SS restraints: 5.69 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 5725 1.02 - 1.22: 5 1.22 - 1.41: 3882 1.41 - 1.61: 5326 1.61 - 1.81: 29 Bond restraints: 14967 Sorted by residual: bond pdb=" C ALA P 130 " pdb=" N PRO P 131 " ideal model delta sigma weight residual 1.334 1.373 -0.039 1.51e-02 4.39e+03 6.50e+00 bond pdb=" C3' DT Y 2 " pdb=" O3' DT Y 2 " ideal model delta sigma weight residual 1.422 1.498 -0.076 3.00e-02 1.11e+03 6.34e+00 bond pdb=" C TYR P 151 " pdb=" N PRO P 152 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.47e+00 bond pdb=" C1' DT Y 2 " pdb=" N1 DT Y 2 " ideal model delta sigma weight residual 1.490 1.552 -0.062 3.00e-02 1.11e+03 4.30e+00 bond pdb=" C4' U W 19 " pdb=" C3' U W 19 " ideal model delta sigma weight residual 1.521 1.491 0.030 1.50e-02 4.44e+03 3.97e+00 ... (remaining 14962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 24434 1.60 - 3.20: 2143 3.20 - 4.79: 239 4.79 - 6.39: 52 6.39 - 7.99: 4 Bond angle restraints: 26872 Sorted by residual: angle pdb=" O3' DT Y 2 " pdb=" C3' DT Y 2 " pdb=" C2' DT Y 2 " ideal model delta sigma weight residual 111.50 119.49 -7.99 1.50e+00 4.44e-01 2.84e+01 angle pdb=" C3' DT Y 2 " pdb=" O3' DT Y 2 " pdb=" P DG Y 3 " ideal model delta sigma weight residual 120.20 127.04 -6.84 1.50e+00 4.44e-01 2.08e+01 angle pdb=" C2' A W 11 " pdb=" C1' A W 11 " pdb=" N9 A W 11 " ideal model delta sigma weight residual 112.00 118.06 -6.06 1.50e+00 4.44e-01 1.63e+01 angle pdb=" C2' A W 251 " pdb=" C1' A W 251 " pdb=" N9 A W 251 " ideal model delta sigma weight residual 112.00 117.64 -5.64 1.50e+00 4.44e-01 1.41e+01 angle pdb=" C5' U W 19 " pdb=" C4' U W 19 " pdb=" O4' U W 19 " ideal model delta sigma weight residual 109.80 115.42 -5.62 1.50e+00 4.44e-01 1.40e+01 ... (remaining 26867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 6434 35.61 - 71.23: 784 71.23 - 106.84: 142 106.84 - 142.46: 1 142.46 - 178.07: 2 Dihedral angle restraints: 7363 sinusoidal: 6260 harmonic: 1103 Sorted by residual: dihedral pdb=" O4' U W 255 " pdb=" C1' U W 255 " pdb=" N1 U W 255 " pdb=" C2 U W 255 " ideal model delta sinusoidal sigma weight residual 232.00 53.93 178.07 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C W 146 " pdb=" C1' C W 146 " pdb=" N1 C W 146 " pdb=" C2 C W 146 " ideal model delta sinusoidal sigma weight residual -128.00 44.32 -172.32 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' C W 147 " pdb=" C1' C W 147 " pdb=" N1 C W 147 " pdb=" C2 C W 147 " ideal model delta sinusoidal sigma weight residual -160.00 -86.23 -73.77 1 1.50e+01 4.44e-03 3.07e+01 ... (remaining 7360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1316 0.052 - 0.104: 319 0.104 - 0.157: 70 0.157 - 0.209: 10 0.209 - 0.261: 7 Chirality restraints: 1722 Sorted by residual: chirality pdb=" C1' A W 11 " pdb=" O4' A W 11 " pdb=" C2' A W 11 " pdb=" N9 A W 11 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C1' A W 251 " pdb=" O4' A W 251 " pdb=" C2' A W 251 " pdb=" N9 A W 251 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C1' A W 189 " pdb=" O4' A W 189 " pdb=" C2' A W 189 " pdb=" N9 A W 189 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1719 not shown) Planarity restraints: 1284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 108 " 0.369 9.50e-02 1.11e+02 1.25e-01 2.38e+01 pdb=" NE ARG P 108 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG P 108 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG P 108 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG P 108 " -0.028 2.00e-02 2.50e+03 pdb="HH11 ARG P 108 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG P 108 " 0.024 2.00e-02 2.50e+03 pdb="HH21 ARG P 108 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG P 108 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 253 " 0.295 9.50e-02 1.11e+02 1.00e-01 1.75e+01 pdb=" NE ARG P 253 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG P 253 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG P 253 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG P 253 " -0.024 2.00e-02 2.50e+03 pdb="HH11 ARG P 253 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG P 253 " 0.025 2.00e-02 2.50e+03 pdb="HH21 ARG P 253 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG P 253 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN P 170 " 0.025 2.00e-02 2.50e+03 3.26e-02 1.59e+01 pdb=" CG ASN P 170 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN P 170 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN P 170 " -0.054 2.00e-02 2.50e+03 pdb="HD21 ASN P 170 " 0.000 2.00e-02 2.50e+03 pdb="HD22 ASN P 170 " 0.049 2.00e-02 2.50e+03 ... (remaining 1281 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 1437 2.26 - 2.85: 24223 2.85 - 3.43: 33487 3.43 - 4.02: 52883 4.02 - 4.60: 74867 Nonbonded interactions: 186897 Sorted by model distance: nonbonded pdb="HO2' A W 152 " pdb=" OP2 U W 154 " model vdw 1.677 2.450 nonbonded pdb="HO2' G W 72 " pdb=" O2 C W 98 " model vdw 1.688 2.450 nonbonded pdb=" HZ1 LYS P 142 " pdb=" OP1 G W 250 " model vdw 1.717 2.450 nonbonded pdb=" O ARG P 108 " pdb=" HG1 THR P 112 " model vdw 1.718 2.450 nonbonded pdb=" OD1 ASP P 91 " pdb=" HZ1 LYS P 136 " model vdw 1.728 2.450 ... (remaining 186892 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.180 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.600 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.005 0.076 9239 Z= 0.250 Angle : 0.905 7.989 13808 Z= 0.533 Chirality : 0.051 0.261 1722 Planarity : 0.014 0.143 751 Dihedral : 23.251 178.072 5273 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.74 % Allowed : 3.70 % Favored : 95.56 % 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: 0.39 (0.46), residues: 324 helix: 0.05 (0.48), residues: 95 sheet: 0.92 (0.62), residues: 76 loop : 0.21 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP P 251 HIS 0.003 0.002 HIS P 78 PHE 0.010 0.002 PHE P 135 TYR 0.018 0.004 TYR P 127 ARG 0.021 0.003 ARG P 263 Details of bonding type rmsd hydrogen bonds : bond 0.10658 ( 401) hydrogen bonds : angle 4.91605 ( 856) covalent geometry : bond 0.00496 ( 9239) covalent geometry : angle 0.90519 (13808) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.9316 time to fit residues: 44.2771 Evaluate side-chains 30 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 226 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 226 HIS P 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.147852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.115129 restraints weight = 27859.373| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.19 r_work: 0.3126 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9239 Z= 0.155 Angle : 0.609 6.289 13808 Z= 0.336 Chirality : 0.037 0.192 1722 Planarity : 0.006 0.043 751 Dihedral : 24.053 177.716 4611 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.11 % Allowed : 5.93 % Favored : 92.96 % 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: 0.93 (0.48), residues: 324 helix: 1.28 (0.50), residues: 98 sheet: 0.40 (0.53), residues: 100 loop : 0.46 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 343 HIS 0.003 0.001 HIS P 226 PHE 0.007 0.001 PHE P 135 TYR 0.010 0.001 TYR P 127 ARG 0.005 0.001 ARG P 79 Details of bonding type rmsd hydrogen bonds : bond 0.05143 ( 401) hydrogen bonds : angle 3.56282 ( 856) covalent geometry : bond 0.00306 ( 9239) covalent geometry : angle 0.60884 (13808) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.706 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.8305 time to fit residues: 30.5554 Evaluate side-chains 29 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 71 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.144710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.112714 restraints weight = 27892.540| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.22 r_work: 0.3065 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9239 Z= 0.209 Angle : 0.614 5.825 13808 Z= 0.335 Chirality : 0.038 0.193 1722 Planarity : 0.006 0.046 751 Dihedral : 24.229 179.343 4609 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.11 % Allowed : 7.41 % Favored : 91.48 % 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: 0.75 (0.46), residues: 324 helix: 1.34 (0.49), residues: 98 sheet: 0.06 (0.52), residues: 96 loop : 0.39 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 289 HIS 0.007 0.003 HIS P 242 PHE 0.014 0.001 PHE P 135 TYR 0.014 0.002 TYR P 127 ARG 0.007 0.001 ARG P 79 Details of bonding type rmsd hydrogen bonds : bond 0.05453 ( 401) hydrogen bonds : angle 3.30364 ( 856) covalent geometry : bond 0.00429 ( 9239) covalent geometry : angle 0.61397 (13808) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.694 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.7913 time to fit residues: 24.8483 Evaluate side-chains 27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 320 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.145397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113643 restraints weight = 27675.454| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.22 r_work: 0.3083 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9239 Z= 0.187 Angle : 0.569 5.278 13808 Z= 0.310 Chirality : 0.036 0.179 1722 Planarity : 0.006 0.039 751 Dihedral : 24.197 179.340 4609 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.48 % Allowed : 7.41 % Favored : 91.11 % 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: 0.82 (0.47), residues: 324 helix: 1.70 (0.50), residues: 98 sheet: -0.07 (0.51), residues: 100 loop : 0.32 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 343 HIS 0.003 0.001 HIS P 165 PHE 0.011 0.001 PHE P 135 TYR 0.009 0.001 TYR P 127 ARG 0.009 0.001 ARG P 79 Details of bonding type rmsd hydrogen bonds : bond 0.05078 ( 401) hydrogen bonds : angle 3.20881 ( 856) covalent geometry : bond 0.00382 ( 9239) covalent geometry : angle 0.56851 (13808) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: P 70 TYR cc_start: 0.7486 (p90) cc_final: 0.7276 (p90) outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.8178 time to fit residues: 27.3073 Evaluate side-chains 28 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 320 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.146841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.114866 restraints weight = 27766.310| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.20 r_work: 0.3114 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9239 Z= 0.123 Angle : 0.533 4.845 13808 Z= 0.295 Chirality : 0.033 0.181 1722 Planarity : 0.005 0.043 751 Dihedral : 24.195 179.508 4609 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.11 % Allowed : 8.52 % Favored : 90.37 % 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: 0.91 (0.48), residues: 324 helix: 1.93 (0.51), residues: 98 sheet: -0.14 (0.50), residues: 100 loop : 0.36 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 343 HIS 0.002 0.001 HIS P 165 PHE 0.011 0.001 PHE P 135 TYR 0.008 0.001 TYR P 46 ARG 0.008 0.001 ARG P 79 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 401) hydrogen bonds : angle 3.09656 ( 856) covalent geometry : bond 0.00242 ( 9239) covalent geometry : angle 0.53317 (13808) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: P 47 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8430 (mt) REVERT: P 70 TYR cc_start: 0.7455 (p90) cc_final: 0.7206 (p90) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 0.7750 time to fit residues: 26.4521 Evaluate side-chains 27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 71 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.143989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.112222 restraints weight = 27872.046| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.20 r_work: 0.3062 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9239 Z= 0.212 Angle : 0.579 4.708 13808 Z= 0.314 Chirality : 0.037 0.165 1722 Planarity : 0.006 0.046 751 Dihedral : 24.218 178.731 4609 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.11 % Allowed : 9.63 % Favored : 89.26 % 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: 0.63 (0.46), residues: 324 helix: 1.68 (0.50), residues: 98 sheet: -0.08 (0.50), residues: 98 loop : -0.02 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP P 289 HIS 0.004 0.002 HIS P 165 PHE 0.014 0.001 PHE P 135 TYR 0.010 0.002 TYR P 127 ARG 0.008 0.001 ARG P 79 Details of bonding type rmsd hydrogen bonds : bond 0.05330 ( 401) hydrogen bonds : angle 3.09600 ( 856) covalent geometry : bond 0.00438 ( 9239) covalent geometry : angle 0.57929 (13808) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.661 Fit side-chains REVERT: P 47 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8549 (mt) REVERT: P 70 TYR cc_start: 0.7447 (p90) cc_final: 0.7179 (p90) outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.8289 time to fit residues: 27.6678 Evaluate side-chains 26 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 320 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.144269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.111990 restraints weight = 27858.468| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.28 r_work: 0.3062 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9239 Z= 0.216 Angle : 0.577 4.685 13808 Z= 0.313 Chirality : 0.037 0.175 1722 Planarity : 0.006 0.074 751 Dihedral : 24.186 178.754 4609 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.11 % Allowed : 9.26 % Favored : 89.63 % 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: 0.52 (0.46), residues: 324 helix: 1.60 (0.50), residues: 98 sheet: -0.09 (0.50), residues: 98 loop : -0.15 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP P 343 HIS 0.004 0.001 HIS P 165 PHE 0.012 0.001 PHE P 135 TYR 0.009 0.002 TYR P 46 ARG 0.007 0.001 ARG P 80 Details of bonding type rmsd hydrogen bonds : bond 0.05259 ( 401) hydrogen bonds : angle 3.10470 ( 856) covalent geometry : bond 0.00445 ( 9239) covalent geometry : angle 0.57653 (13808) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.729 Fit side-chains REVERT: P 47 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8548 (mt) REVERT: P 70 TYR cc_start: 0.7475 (p90) cc_final: 0.7191 (p90) outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.8589 time to fit residues: 26.5373 Evaluate side-chains 26 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 320 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 53 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.145047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108758 restraints weight = 27630.324| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 0.70 r_work: 0.3159 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9239 Z= 0.157 Angle : 0.547 4.624 13808 Z= 0.301 Chirality : 0.035 0.176 1722 Planarity : 0.006 0.058 751 Dihedral : 24.192 178.700 4609 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.11 % Allowed : 9.26 % Favored : 89.63 % 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: 0.62 (0.47), residues: 324 helix: 1.72 (0.51), residues: 98 sheet: -0.05 (0.50), residues: 98 loop : -0.10 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 343 HIS 0.003 0.001 HIS P 165 PHE 0.012 0.001 PHE P 135 TYR 0.009 0.001 TYR P 46 ARG 0.011 0.000 ARG P 80 Details of bonding type rmsd hydrogen bonds : bond 0.04930 ( 401) hydrogen bonds : angle 3.06642 ( 856) covalent geometry : bond 0.00317 ( 9239) covalent geometry : angle 0.54749 (13808) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: P 47 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8542 (mt) REVERT: P 70 TYR cc_start: 0.7489 (p90) cc_final: 0.7189 (p90) outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.8589 time to fit residues: 26.7040 Evaluate side-chains 27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 320 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 0.0670 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 10.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.144220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.112324 restraints weight = 27721.566| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.21 r_work: 0.3079 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9239 Z= 0.178 Angle : 0.552 4.542 13808 Z= 0.301 Chirality : 0.035 0.176 1722 Planarity : 0.006 0.063 751 Dihedral : 24.168 178.902 4609 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.48 % Allowed : 8.89 % Favored : 89.63 % 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: 0.62 (0.46), residues: 324 helix: 1.76 (0.51), residues: 98 sheet: -0.06 (0.50), residues: 98 loop : -0.14 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 343 HIS 0.003 0.001 HIS P 165 PHE 0.010 0.001 PHE P 135 TYR 0.009 0.001 TYR P 46 ARG 0.006 0.000 ARG P 80 Details of bonding type rmsd hydrogen bonds : bond 0.04994 ( 401) hydrogen bonds : angle 3.06747 ( 856) covalent geometry : bond 0.00368 ( 9239) covalent geometry : angle 0.55182 (13808) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: P 47 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8537 (mt) REVERT: P 70 TYR cc_start: 0.7464 (p90) cc_final: 0.7164 (p90) outliers start: 4 outliers final: 3 residues processed: 26 average time/residue: 0.8763 time to fit residues: 26.9583 Evaluate side-chains 27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 320 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.142421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110274 restraints weight = 27597.675| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.27 r_work: 0.3042 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9239 Z= 0.236 Angle : 0.604 4.681 13808 Z= 0.326 Chirality : 0.038 0.177 1722 Planarity : 0.007 0.072 751 Dihedral : 24.258 177.014 4609 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.48 % Allowed : 9.26 % Favored : 89.26 % 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: 0.28 (0.45), residues: 324 helix: 1.48 (0.50), residues: 98 sheet: -0.15 (0.50), residues: 98 loop : -0.44 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP P 343 HIS 0.005 0.002 HIS P 165 PHE 0.014 0.001 PHE P 135 TYR 0.010 0.002 TYR P 127 ARG 0.009 0.001 ARG P 80 Details of bonding type rmsd hydrogen bonds : bond 0.05646 ( 401) hydrogen bonds : angle 3.16456 ( 856) covalent geometry : bond 0.00487 ( 9239) covalent geometry : angle 0.60394 (13808) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: P 47 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8577 (mt) REVERT: P 70 TYR cc_start: 0.7479 (p90) cc_final: 0.7231 (p90) outliers start: 4 outliers final: 2 residues processed: 26 average time/residue: 0.9638 time to fit residues: 29.4711 Evaluate side-chains 26 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 71 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 0.0770 chunk 54 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.145858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114368 restraints weight = 27920.348| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.25 r_work: 0.3098 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9239 Z= 0.126 Angle : 0.533 4.234 13808 Z= 0.292 Chirality : 0.033 0.180 1722 Planarity : 0.005 0.070 751 Dihedral : 24.091 178.461 4609 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.11 % Allowed : 9.63 % Favored : 89.26 % 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: 0.71 (0.47), residues: 324 helix: 1.93 (0.51), residues: 98 sheet: 0.04 (0.50), residues: 98 loop : -0.23 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 343 HIS 0.002 0.001 HIS P 165 PHE 0.007 0.001 PHE P 135 TYR 0.008 0.001 TYR P 46 ARG 0.007 0.000 ARG P 80 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 401) hydrogen bonds : angle 3.00666 ( 856) covalent geometry : bond 0.00252 ( 9239) covalent geometry : angle 0.53251 (13808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7113.65 seconds wall clock time: 122 minutes 35.67 seconds (7355.67 seconds total)