Starting phenix.real_space_refine on Sat Mar 16 17:38:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/03_2024/6c4h_7340_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/03_2024/6c4h_7340.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/03_2024/6c4h_7340_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/03_2024/6c4h_7340_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/03_2024/6c4h_7340_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/03_2024/6c4h_7340.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/03_2024/6c4h_7340.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/03_2024/6c4h_7340_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/03_2024/6c4h_7340_updated.pdb" } 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= 0.012 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: 6 Type Number sf(0) Gaussians P 647 5.49 5 Mg 34 5.21 5 S 6 5.16 5 C 7066 2.51 5 N 2808 2.21 5 O 4765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 212": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N GLU 90": "OE1" <-> "OE2" Residue "X ARG 11": "NH1" <-> "NH2" Residue "v ARG 256": "NH1" <-> "NH2" Residue "v ARG 262": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15326 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 13622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 13622 Classifications: {'RNA': 636} Modifications used: {'rna2p': 4, 'rna2p_pur': 71, 'rna2p_pyr': 31, 'rna3p': 13, 'rna3p_pur': 274, 'rna3p_pyr': 243} Link IDs: {'rna2p': 106, 'rna3p': 529} Chain breaks: 9 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 5, 'TRANS': 41} Chain: "D" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "N" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 125 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "X" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "x" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 252 Classifications: {'RNA': 12} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna3p': 11} Chain breaks: 1 Chain: "v" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 496 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Unusual residues: {' MG': 34} Classifications: {'undetermined': 34} Link IDs: {None: 33} Time building chain proxies: 8.81, per 1000 atoms: 0.57 Number of scatterers: 15326 At special positions: 0 Unit cell: (132, 104.4, 133.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 6 16.00 P 647 15.00 Mg 34 11.99 O 4765 8.00 N 2808 7.00 C 7066 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 - 3.50 Amino acid : False - 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: 10.23 Conformation dependent library (CDL) restraints added in 613.3 milliseconds 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 4 helices and 1 sheets defined 14.1% alpha, 7.6% beta 174 base pairs and 273 stacking pairs defined. Time for finding SS restraints: 10.11 Creating SS restraints... Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'D' and resid 121 through 124 No H-bonds generated for 'chain 'D' and resid 121 through 124' Processing helix chain 'v' and resid 253 through 255 No H-bonds generated for 'chain 'v' and resid 253 through 255' Processing helix chain 'v' and resid 280 through 295 Processing sheet with id= A, first strand: chain 'v' and resid 239 through 244 24 hydrogen bonds defined for protein. 66 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 444 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 174 basepair parallelities 273 stacking parallelities Total time for adding SS restraints: 10.65 Time building geometry restraints manager: 10.70 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: 1726 1.33 - 1.45: 8157 1.45 - 1.57: 5781 1.57 - 1.69: 1283 1.69 - 1.81: 11 Bond restraints: 16958 Sorted by residual: bond pdb=" C4 5MU A 747 " pdb=" C5 5MU A 747 " ideal model delta sigma weight residual 1.802 1.490 0.312 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.490 0.312 2.00e-02 2.50e+03 2.43e+02 bond pdb=" N1 5MU A1939 " pdb=" C6 5MU A1939 " ideal model delta sigma weight residual 1.635 1.344 0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" N1 5MU A 747 " pdb=" C6 5MU A 747 " ideal model delta sigma weight residual 1.635 1.346 0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C5 5MU A 747 " pdb=" C6 5MU A 747 " ideal model delta sigma weight residual 1.155 1.397 -0.242 2.00e-02 2.50e+03 1.47e+02 ... (remaining 16953 not shown) Histogram of bond angle deviations from ideal: 94.08 - 102.59: 1174 102.59 - 111.11: 9982 111.11 - 119.63: 7739 119.63 - 128.14: 6238 128.14 - 136.66: 959 Bond angle restraints: 26092 Sorted by residual: angle pdb=" O2' G7M A2069 " pdb=" C2' G7M A2069 " pdb=" C1' G7M A2069 " ideal model delta sigma weight residual 108.40 128.85 -20.45 1.50e+00 4.44e-01 1.86e+02 angle pdb=" C3' G7M A2069 " pdb=" C2' G7M A2069 " pdb=" O2' G7M A2069 " ideal model delta sigma weight residual 110.70 127.84 -17.14 1.50e+00 4.44e-01 1.31e+02 angle pdb=" C4' G7M A2069 " pdb=" O4' G7M A2069 " pdb=" C1' G7M A2069 " ideal model delta sigma weight residual 109.90 99.64 10.26 1.00e+00 1.00e+00 1.05e+02 angle pdb=" C2' G7M A2069 " pdb=" C1' G7M A2069 " pdb=" N9 G7M A2069 " ideal model delta sigma weight residual 112.00 126.16 -14.16 1.50e+00 4.44e-01 8.91e+01 angle pdb=" N ARG C 212 " pdb=" CA ARG C 212 " pdb=" C ARG C 212 " ideal model delta sigma weight residual 113.50 103.34 10.16 1.23e+00 6.61e-01 6.82e+01 ... (remaining 26087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.55: 9009 32.55 - 65.10: 1607 65.10 - 97.65: 258 97.65 - 130.21: 6 130.21 - 162.76: 1 Dihedral angle restraints: 10881 sinusoidal: 10380 harmonic: 501 Sorted by residual: dihedral pdb=" O4' U A2585 " pdb=" C1' U A2585 " pdb=" N1 U A2585 " pdb=" C2 U A2585 " ideal model delta sinusoidal sigma weight residual -128.00 34.76 -162.76 1 1.70e+01 3.46e-03 6.49e+01 dihedral pdb=" C5' G A 748 " pdb=" C4' G A 748 " pdb=" C3' G A 748 " pdb=" O3' G A 748 " ideal model delta sinusoidal sigma weight residual 147.00 104.39 42.61 1 8.00e+00 1.56e-02 3.96e+01 dihedral pdb=" O4' U A 790 " pdb=" C1' U A 790 " pdb=" N1 U A 790 " pdb=" C2 U A 790 " ideal model delta sinusoidal sigma weight residual -160.00 -81.05 -78.95 1 1.50e+01 4.44e-03 3.45e+01 ... (remaining 10878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.303: 3382 0.303 - 0.606: 10 0.606 - 0.909: 0 0.909 - 1.212: 1 1.212 - 1.514: 1 Chirality restraints: 3394 Sorted by residual: chirality pdb=" C2' G7M A2069 " pdb=" C3' G7M A2069 " pdb=" O2' G7M A2069 " pdb=" C1' G7M A2069 " both_signs ideal model delta sigma weight residual False -2.75 -1.24 -1.51 2.00e-01 2.50e+01 5.73e+01 chirality pdb=" C1' G7M A2069 " pdb=" O4' G7M A2069 " pdb=" C2' G7M A2069 " pdb=" N9 G7M A2069 " both_signs ideal model delta sigma weight residual False 2.46 1.51 0.95 2.00e-01 2.50e+01 2.26e+01 chirality pdb=" C4' G7M A2069 " pdb=" C5' G7M A2069 " pdb=" O4' G7M A2069 " pdb=" C3' G7M A2069 " both_signs ideal model delta sigma weight residual False -2.50 -1.94 -0.56 2.00e-01 2.50e+01 7.87e+00 ... (remaining 3391 not shown) Planarity restraints: 911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC A2498 " 0.036 2.00e-02 2.50e+03 6.06e-01 8.28e+03 pdb=" C4' OMC A2498 " -0.480 2.00e-02 2.50e+03 pdb=" O4' OMC A2498 " -0.787 2.00e-02 2.50e+03 pdb=" C3' OMC A2498 " 0.553 2.00e-02 2.50e+03 pdb=" O3' OMC A2498 " 0.603 2.00e-02 2.50e+03 pdb=" C2' OMC A2498 " 0.206 2.00e-02 2.50e+03 pdb=" O2' OMC A2498 " -0.885 2.00e-02 2.50e+03 pdb=" C1' OMC A2498 " -0.208 2.00e-02 2.50e+03 pdb=" N1 OMC A2498 " 0.961 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2251 " 0.025 2.00e-02 2.50e+03 5.86e-01 7.73e+03 pdb=" C4' OMG A2251 " -0.470 2.00e-02 2.50e+03 pdb=" O4' OMG A2251 " -0.752 2.00e-02 2.50e+03 pdb=" C3' OMG A2251 " 0.572 2.00e-02 2.50e+03 pdb=" O3' OMG A2251 " 0.579 2.00e-02 2.50e+03 pdb=" C2' OMG A2251 " 0.212 2.00e-02 2.50e+03 pdb=" O2' OMG A2251 " -0.848 2.00e-02 2.50e+03 pdb=" C1' OMG A2251 " -0.229 2.00e-02 2.50e+03 pdb=" N9 OMG A2251 " 0.910 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2445 " 0.112 2.00e-02 2.50e+03 5.86e-01 7.72e+03 pdb=" C4' 2MG A2445 " -0.514 2.00e-02 2.50e+03 pdb=" O4' 2MG A2445 " -0.864 2.00e-02 2.50e+03 pdb=" C3' 2MG A2445 " 0.514 2.00e-02 2.50e+03 pdb=" O3' 2MG A2445 " 0.483 2.00e-02 2.50e+03 pdb=" C2' 2MG A2445 " 0.271 2.00e-02 2.50e+03 pdb=" O2' 2MG A2445 " -0.724 2.00e-02 2.50e+03 pdb=" C1' 2MG A2445 " -0.234 2.00e-02 2.50e+03 pdb=" N9 2MG A2445 " 0.956 2.00e-02 2.50e+03 ... (remaining 908 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 83 2.51 - 3.11: 9765 3.11 - 3.71: 33488 3.71 - 4.30: 46469 4.30 - 4.90: 56548 Nonbonded interactions: 146353 Sorted by model distance: nonbonded pdb=" OP2 A A2518 " pdb="MG MG A3021 " model vdw 1.913 2.170 nonbonded pdb=" OP2 C A 740 " pdb="MG MG A3002 " model vdw 1.915 2.170 nonbonded pdb=" OP2 OMC A2498 " pdb="MG MG A3019 " model vdw 1.918 2.170 nonbonded pdb=" OP2 C A2499 " pdb="MG MG A3019 " model vdw 1.946 2.170 nonbonded pdb=" OP2 U A 963 " pdb="MG MG A3005 " model vdw 1.948 2.170 ... (remaining 146348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.310 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 58.130 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 0.312 16958 Z= 0.600 Angle : 1.184 20.453 26092 Z= 0.759 Chirality : 0.108 1.514 3394 Planarity : 0.048 0.606 911 Dihedral : 25.151 162.758 10561 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 6.80 % Allowed : 18.37 % Favored : 74.83 % Cbeta Deviations : 0.62 % 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: -2.61 (0.55), residues: 171 helix: -0.18 (0.90), residues: 28 sheet: -1.46 (1.10), residues: 15 loop : -2.33 (0.48), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 248 HIS 0.006 0.002 HIS C 230 PHE 0.014 0.003 PHE D 127 TYR 0.006 0.002 TYR v 244 ARG 0.024 0.004 ARG v 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 19 time to evaluate : 0.595 Fit side-chains REVERT: C 216 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8700 (p) REVERT: N 84 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8088 (mtmm) REVERT: X 17 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5049 (pp20) outliers start: 10 outliers final: 1 residues processed: 29 average time/residue: 0.5428 time to fit residues: 20.1016 Evaluate side-chains 21 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 17 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain X residue 17 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN D 136 ASN D 140 HIS D 148 GLN ** v 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 273 GLN v 281 HIS v 283 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16958 Z= 0.167 Angle : 0.817 15.937 26092 Z= 0.466 Chirality : 0.034 0.496 3394 Planarity : 0.011 0.126 911 Dihedral : 24.581 168.014 10219 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.08 % Allowed : 17.69 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.62), residues: 171 helix: 2.81 (1.23), residues: 24 sheet: -1.97 (0.98), residues: 20 loop : -1.98 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 213 HIS 0.004 0.001 HIS C 230 PHE 0.009 0.002 PHE D 127 TYR 0.001 0.000 TYR v 296 ARG 0.005 0.001 ARG v 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 0.636 Fit side-chains REVERT: D 141 ARG cc_start: 0.9109 (mtp-110) cc_final: 0.8903 (mtp-110) REVERT: N 84 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8333 (mtmm) REVERT: X 17 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5214 (pp20) outliers start: 6 outliers final: 3 residues processed: 22 average time/residue: 0.3754 time to fit residues: 11.7799 Evaluate side-chains 23 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain v residue 263 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 0.0050 overall best weight: 4.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 ASN D 148 GLN D 150 GLN ** v 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 16958 Z= 0.507 Angle : 0.971 13.806 26092 Z= 0.525 Chirality : 0.046 0.494 3394 Planarity : 0.013 0.140 911 Dihedral : 24.342 156.895 10218 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 8.84 % Allowed : 17.69 % Favored : 73.47 % 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: -1.98 (0.58), residues: 171 helix: 1.50 (1.06), residues: 24 sheet: -1.60 (1.12), residues: 20 loop : -1.99 (0.49), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP C 248 HIS 0.005 0.001 HIS C 230 PHE 0.008 0.002 PHE D 127 TYR 0.008 0.002 TYR v 244 ARG 0.005 0.001 ARG v 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 16 time to evaluate : 0.597 Fit side-chains REVERT: N 84 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8267 (mtmm) REVERT: X 17 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5210 (pp20) REVERT: v 291 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7287 (tpp) outliers start: 13 outliers final: 7 residues processed: 26 average time/residue: 0.4158 time to fit residues: 14.8076 Evaluate side-chains 25 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 15 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain v residue 262 ARG Chi-restraints excluded: chain v residue 263 ILE Chi-restraints excluded: chain v residue 271 VAL Chi-restraints excluded: chain v residue 291 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 16958 Z= 0.405 Angle : 0.889 14.002 26092 Z= 0.491 Chirality : 0.041 0.493 3394 Planarity : 0.012 0.134 911 Dihedral : 24.211 154.829 10218 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 6.80 % Allowed : 21.09 % Favored : 72.11 % 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: -2.00 (0.58), residues: 171 helix: 1.00 (1.02), residues: 24 sheet: -1.48 (1.16), residues: 20 loop : -1.92 (0.49), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 248 HIS 0.004 0.001 HIS C 230 PHE 0.005 0.002 PHE D 127 TYR 0.005 0.001 TYR v 244 ARG 0.003 0.001 ARG v 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 16 time to evaluate : 0.600 Fit side-chains REVERT: X 17 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5159 (pp20) REVERT: v 291 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7384 (tpp) outliers start: 10 outliers final: 6 residues processed: 23 average time/residue: 0.4197 time to fit residues: 13.2585 Evaluate side-chains 24 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 16 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain v residue 263 ILE Chi-restraints excluded: chain v residue 282 LYS Chi-restraints excluded: chain v residue 291 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 16958 Z= 0.452 Angle : 0.920 14.336 26092 Z= 0.504 Chirality : 0.043 0.522 3394 Planarity : 0.012 0.137 911 Dihedral : 24.185 152.805 10218 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 8.16 % Allowed : 21.09 % Favored : 70.75 % 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: -2.13 (0.57), residues: 171 helix: 0.61 (1.03), residues: 24 sheet: -1.73 (1.09), residues: 20 loop : -1.91 (0.49), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 248 HIS 0.005 0.001 HIS C 230 PHE 0.008 0.002 PHE D 127 TYR 0.005 0.001 TYR v 244 ARG 0.004 0.001 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 15 time to evaluate : 0.590 Fit side-chains REVERT: X 17 GLU cc_start: 0.6109 (OUTLIER) cc_final: 0.5198 (pp20) REVERT: v 291 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7435 (tpp) outliers start: 12 outliers final: 8 residues processed: 24 average time/residue: 0.4094 time to fit residues: 13.5749 Evaluate side-chains 25 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 15 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 LYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain v residue 254 VAL Chi-restraints excluded: chain v residue 262 ARG Chi-restraints excluded: chain v residue 282 LYS Chi-restraints excluded: chain v residue 291 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 0.0770 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 overall best weight: 2.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16958 Z= 0.321 Angle : 0.849 14.421 26092 Z= 0.476 Chirality : 0.038 0.511 3394 Planarity : 0.012 0.131 911 Dihedral : 24.141 153.353 10218 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 6.80 % Allowed : 21.77 % Favored : 71.43 % 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: -2.02 (0.59), residues: 171 helix: 0.81 (1.08), residues: 24 sheet: -1.80 (1.11), residues: 20 loop : -1.83 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 248 HIS 0.004 0.001 HIS C 230 PHE 0.004 0.001 PHE D 127 TYR 0.003 0.001 TYR v 244 ARG 0.003 0.001 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 15 time to evaluate : 0.555 Fit side-chains REVERT: X 17 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5094 (pp20) REVERT: v 291 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7286 (tpp) outliers start: 10 outliers final: 7 residues processed: 23 average time/residue: 0.4693 time to fit residues: 14.4564 Evaluate side-chains 23 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 14 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain v residue 262 ARG Chi-restraints excluded: chain v residue 263 ILE Chi-restraints excluded: chain v residue 282 LYS Chi-restraints excluded: chain v residue 291 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 0.0370 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 16958 Z= 0.427 Angle : 0.903 14.353 26092 Z= 0.496 Chirality : 0.042 0.499 3394 Planarity : 0.012 0.136 911 Dihedral : 24.118 155.831 10218 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.12 % Allowed : 24.49 % Favored : 69.39 % 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: -2.11 (0.58), residues: 171 helix: 0.73 (1.09), residues: 24 sheet: -1.85 (1.10), residues: 20 loop : -1.90 (0.49), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 248 HIS 0.005 0.001 HIS C 230 PHE 0.004 0.001 PHE D 118 TYR 0.005 0.001 TYR v 244 ARG 0.004 0.001 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 14 time to evaluate : 0.588 Fit side-chains REVERT: N 84 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8294 (mptt) REVERT: X 17 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5140 (pp20) REVERT: v 291 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7374 (tpp) outliers start: 9 outliers final: 6 residues processed: 21 average time/residue: 0.4099 time to fit residues: 12.0531 Evaluate side-chains 23 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 14 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain v residue 262 ARG Chi-restraints excluded: chain v residue 263 ILE Chi-restraints excluded: chain v residue 282 LYS Chi-restraints excluded: chain v residue 291 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 0.0980 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 0.1980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16958 Z= 0.347 Angle : 0.863 14.513 26092 Z= 0.481 Chirality : 0.039 0.510 3394 Planarity : 0.012 0.133 911 Dihedral : 24.145 156.862 10218 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.12 % Allowed : 25.17 % Favored : 68.71 % 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: -2.06 (0.59), residues: 171 helix: 0.76 (1.10), residues: 24 sheet: -1.87 (1.10), residues: 20 loop : -1.85 (0.49), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 248 HIS 0.003 0.001 HIS v 281 PHE 0.004 0.001 PHE C 240 TYR 0.004 0.001 TYR v 244 ARG 0.004 0.001 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 14 time to evaluate : 0.666 Fit side-chains REVERT: X 17 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5066 (pp20) REVERT: v 291 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7359 (tpp) outliers start: 9 outliers final: 7 residues processed: 21 average time/residue: 0.3981 time to fit residues: 11.6673 Evaluate side-chains 23 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 14 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain v residue 262 ARG Chi-restraints excluded: chain v residue 263 ILE Chi-restraints excluded: chain v residue 282 LYS Chi-restraints excluded: chain v residue 291 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 16958 Z= 0.425 Angle : 0.904 14.367 26092 Z= 0.497 Chirality : 0.042 0.504 3394 Planarity : 0.012 0.135 911 Dihedral : 24.121 166.350 10218 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 7.48 % Allowed : 24.49 % Favored : 68.03 % 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: -2.15 (0.58), residues: 171 helix: 0.65 (1.11), residues: 24 sheet: -1.77 (1.10), residues: 20 loop : -1.94 (0.49), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 248 HIS 0.004 0.001 HIS C 230 PHE 0.004 0.001 PHE D 156 TYR 0.005 0.001 TYR v 244 ARG 0.004 0.001 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 14 time to evaluate : 0.620 Fit side-chains REVERT: X 17 GLU cc_start: 0.6080 (OUTLIER) cc_final: 0.5142 (pp20) REVERT: v 291 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7377 (tpp) outliers start: 11 outliers final: 9 residues processed: 22 average time/residue: 0.4071 time to fit residues: 12.5755 Evaluate side-chains 25 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 14 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain v residue 254 VAL Chi-restraints excluded: chain v residue 262 ARG Chi-restraints excluded: chain v residue 263 ILE Chi-restraints excluded: chain v residue 282 LYS Chi-restraints excluded: chain v residue 291 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 0.0010 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16958 Z= 0.282 Angle : 0.826 14.458 26092 Z= 0.466 Chirality : 0.037 0.502 3394 Planarity : 0.012 0.127 911 Dihedral : 24.076 152.039 10218 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 6.12 % Allowed : 25.85 % Favored : 68.03 % 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: -2.00 (0.59), residues: 171 helix: 0.82 (1.13), residues: 24 sheet: -1.78 (1.09), residues: 20 loop : -1.82 (0.49), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 248 HIS 0.003 0.001 HIS C 230 PHE 0.003 0.001 PHE C 240 TYR 0.003 0.001 TYR v 244 ARG 0.003 0.000 ARG D 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 14 time to evaluate : 0.645 Fit side-chains REVERT: X 17 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5094 (pp20) REVERT: v 291 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7349 (tpp) outliers start: 9 outliers final: 7 residues processed: 21 average time/residue: 0.4308 time to fit residues: 12.7728 Evaluate side-chains 23 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 14 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain v residue 262 ARG Chi-restraints excluded: chain v residue 263 ILE Chi-restraints excluded: chain v residue 282 LYS Chi-restraints excluded: chain v residue 291 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 26 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.119472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.108510 restraints weight = 22933.878| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 0.64 r_work: 0.3044 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 16958 Z= 0.476 Angle : 0.931 14.378 26092 Z= 0.507 Chirality : 0.043 0.507 3394 Planarity : 0.013 0.138 911 Dihedral : 24.103 148.757 10218 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 7.48 % Allowed : 24.49 % Favored : 68.03 % 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: -2.19 (0.58), residues: 171 helix: 0.49 (1.12), residues: 24 sheet: -1.79 (1.09), residues: 20 loop : -1.93 (0.48), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 248 HIS 0.006 0.001 HIS C 230 PHE 0.005 0.001 PHE D 118 TYR 0.006 0.002 TYR v 244 ARG 0.004 0.001 ARG D 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1967.80 seconds wall clock time: 37 minutes 14.14 seconds (2234.14 seconds total)