Starting phenix.real_space_refine on Tue Feb 13 10:59:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef9_28075/02_2024/8ef9_28075_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef9_28075/02_2024/8ef9_28075.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef9_28075/02_2024/8ef9_28075_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef9_28075/02_2024/8ef9_28075_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef9_28075/02_2024/8ef9_28075_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef9_28075/02_2024/8ef9_28075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef9_28075/02_2024/8ef9_28075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef9_28075/02_2024/8ef9_28075_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef9_28075/02_2024/8ef9_28075_updated.pdb" } resolution = 2.4 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= -0.001 sd= 0.163 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 311 atoms to isotropic. 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 27 5.49 5 Mg 1 5.21 5 S 28 5.16 5 C 3234 2.51 5 N 923 2.21 5 O 1027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5240 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4715 Classifications: {'peptide': 599} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 575} Chain breaks: 6 Chain: "E" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 267 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 226 Unusual residues: {'2DA': 1} Classifications: {'DNA': 11, 'undetermined': 1} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 10, None: 1} Not linked: pdbres=" DG F 19 " pdbres="2DA F 20 " Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'DGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG B MG A2802 " occ=0.50 Time building chain proxies: 3.72, per 1000 atoms: 0.71 Number of scatterers: 5240 At special positions: 0 Unit cell: (74.2, 76.32, 97.52, 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 28 16.00 P 27 15.00 Mg 1 11.99 O 1027 8.00 N 923 7.00 C 3234 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 888.1 milliseconds 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 5 sheets defined 51.9% alpha, 8.3% beta 10 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 1989 through 2001 removed outlier: 3.910A pdb=" N THR A2001 " --> pdb=" O LYS A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2105 Processing helix chain 'A' and resid 2122 through 2133 Processing helix chain 'A' and resid 2144 through 2151 Processing helix chain 'A' and resid 2160 through 2167 Processing helix chain 'A' and resid 2169 through 2174 Proline residue: A2173 - end of helix Processing helix chain 'A' and resid 2186 through 2210 removed outlier: 3.655A pdb=" N GLY A2206 " --> pdb=" O ASN A2202 " (cutoff:3.500A) Processing helix chain 'A' and resid 2214 through 2219 Processing helix chain 'A' and resid 2221 through 2234 Processing helix chain 'A' and resid 2240 through 2265 Processing helix chain 'A' and resid 2274 through 2278 Processing helix chain 'A' and resid 2322 through 2325 Processing helix chain 'A' and resid 2333 through 2358 removed outlier: 5.235A pdb=" N PHE A2353 " --> pdb=" O THR A2349 " (cutoff:3.500A) Proline residue: A2354 - end of helix Processing helix chain 'A' and resid 2390 through 2392 No H-bonds generated for 'chain 'A' and resid 2390 through 2392' Processing helix chain 'A' and resid 2447 through 2450 Processing helix chain 'A' and resid 2467 through 2476 Processing helix chain 'A' and resid 2479 through 2485 Processing helix chain 'A' and resid 2491 through 2500 Processing helix chain 'A' and resid 2504 through 2506 No H-bonds generated for 'chain 'A' and resid 2504 through 2506' Processing helix chain 'A' and resid 2509 through 2523 Processing helix chain 'A' and resid 2528 through 2535 Processing helix chain 'A' and resid 2539 through 2552 Processing helix chain 'A' and resid 2554 through 2570 Processing helix chain 'A' and resid 2584 through 2587 Processing helix chain 'A' and resid 2591 through 2628 Processing helix chain 'A' and resid 2675 through 2688 Processing sheet with id= A, first strand: chain 'A' and resid 1981 through 1984 removed outlier: 4.085A pdb=" N ASP A2065 " --> pdb=" O TRP A2061 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRP A2061 " --> pdb=" O ASP A2065 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA A2010 " --> pdb=" O ILE A2055 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU A2057 " --> pdb=" O ALA A2008 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA A2008 " --> pdb=" O LEU A2057 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL A2059 " --> pdb=" O SER A2006 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER A2006 " --> pdb=" O VAL A2059 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TRP A2061 " --> pdb=" O ARG A2004 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N ARG A2004 " --> pdb=" O TRP A2061 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A2116 " --> pdb=" O TYR A2005 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU A2007 " --> pdb=" O VAL A2116 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL A2118 " --> pdb=" O LEU A2007 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LEU A2009 " --> pdb=" O VAL A2118 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 2359 through 2362 Processing sheet with id= C, first strand: chain 'A' and resid 2397 through 2399 Processing sheet with id= D, first strand: chain 'A' and resid 2698 through 2703 Processing sheet with id= E, first strand: chain 'A' and resid 2572 through 2574 231 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 806 1.27 - 1.40: 1340 1.40 - 1.54: 3111 1.54 - 1.68: 84 1.68 - 1.81: 41 Bond restraints: 5382 Sorted by residual: bond pdb=" C4' 2DA F 20 " pdb=" C3' 2DA F 20 " ideal model delta sigma weight residual 1.625 1.281 0.344 2.00e-02 2.50e+03 2.95e+02 bond pdb=" C4' 2DA F 20 " pdb=" O4' 2DA F 20 " ideal model delta sigma weight residual 1.288 1.618 -0.330 2.00e-02 2.50e+03 2.72e+02 bond pdb=" C3' 2DA F 20 " pdb=" C2' 2DA F 20 " ideal model delta sigma weight residual 1.271 1.524 -0.253 2.00e-02 2.50e+03 1.61e+02 bond pdb=" O4' 2DA F 20 " pdb=" C1' 2DA F 20 " ideal model delta sigma weight residual 1.525 1.282 0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C2' DGT A2801 " pdb=" C3' DGT A2801 " ideal model delta sigma weight residual 1.284 1.519 -0.235 2.00e-02 2.50e+03 1.38e+02 ... (remaining 5377 not shown) Histogram of bond angle deviations from ideal: 98.05 - 107.07: 303 107.07 - 116.09: 3434 116.09 - 125.11: 3493 125.11 - 134.13: 153 134.13 - 143.15: 2 Bond angle restraints: 7385 Sorted by residual: angle pdb=" CA ASP A2463 " pdb=" CB ASP A2463 " pdb=" CG ASP A2463 " ideal model delta sigma weight residual 112.60 119.63 -7.03 1.00e+00 1.00e+00 4.94e+01 angle pdb=" PB DGT A2801 " pdb=" O3B DGT A2801 " pdb=" PG DGT A2801 " ideal model delta sigma weight residual 123.56 143.15 -19.59 3.00e+00 1.11e-01 4.26e+01 angle pdb=" PA DGT A2801 " pdb=" O3A DGT A2801 " pdb=" PB DGT A2801 " ideal model delta sigma weight residual 123.57 141.45 -17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" O1A DGT A2801 " pdb=" PA DGT A2801 " pdb=" O3A DGT A2801 " ideal model delta sigma weight residual 109.45 98.05 11.40 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C ILE A2667 " pdb=" N TYR A2668 " pdb=" CA TYR A2668 " ideal model delta sigma weight residual 122.42 115.71 6.71 1.77e+00 3.19e-01 1.44e+01 ... (remaining 7380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.38: 2952 29.38 - 58.76: 200 58.76 - 88.14: 22 88.14 - 117.52: 0 117.52 - 146.91: 1 Dihedral angle restraints: 3175 sinusoidal: 1436 harmonic: 1739 Sorted by residual: dihedral pdb=" CA ALA A2278 " pdb=" C ALA A2278 " pdb=" N GLN A2279 " pdb=" CA GLN A2279 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" O1B DGT A2801 " pdb=" O3B DGT A2801 " pdb=" PB DGT A2801 " pdb=" PG DGT A2801 " ideal model delta sinusoidal sigma weight residual 301.68 154.77 146.91 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" CA THR A2386 " pdb=" C THR A2386 " pdb=" N GLU A2387 " pdb=" CA GLU A2387 " ideal model delta harmonic sigma weight residual -180.00 -159.66 -20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 3172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 645 0.046 - 0.093: 158 0.093 - 0.139: 32 0.139 - 0.186: 9 0.186 - 0.232: 1 Chirality restraints: 845 Sorted by residual: chirality pdb=" CA TYR A2668 " pdb=" N TYR A2668 " pdb=" C TYR A2668 " pdb=" CB TYR A2668 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASP A2463 " pdb=" N ASP A2463 " pdb=" C ASP A2463 " pdb=" CB ASP A2463 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA ILE A2667 " pdb=" N ILE A2667 " pdb=" C ILE A2667 " pdb=" CB ILE A2667 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.25e-01 ... (remaining 842 not shown) Planarity restraints: 852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DGT A2801 " -0.119 2.00e-02 2.50e+03 5.03e-02 7.59e+01 pdb=" C2 DGT A2801 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DGT A2801 " 0.029 2.00e-02 2.50e+03 pdb=" C5 DGT A2801 " 0.011 2.00e-02 2.50e+03 pdb=" C6 DGT A2801 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DGT A2801 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DGT A2801 " -0.035 2.00e-02 2.50e+03 pdb=" N2 DGT A2801 " -0.012 2.00e-02 2.50e+03 pdb=" N3 DGT A2801 " 0.063 2.00e-02 2.50e+03 pdb=" N7 DGT A2801 " 0.021 2.00e-02 2.50e+03 pdb=" N9 DGT A2801 " 0.079 2.00e-02 2.50e+03 pdb=" O6 DGT A2801 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A2463 " -0.021 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C ASP A2463 " 0.076 2.00e-02 2.50e+03 pdb=" O ASP A2463 " -0.031 2.00e-02 2.50e+03 pdb=" N TYR A2464 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A2160 " 0.059 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO A2161 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A2161 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A2161 " 0.049 5.00e-02 4.00e+02 ... (remaining 849 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 26 2.55 - 3.13: 3966 3.13 - 3.72: 8897 3.72 - 4.31: 12913 4.31 - 4.90: 20003 Nonbonded interactions: 45805 Sorted by model distance: nonbonded pdb=" OD1 ASP A2463 " pdb="MG B MG A2802 " model vdw 1.958 2.170 nonbonded pdb=" O TYR A2464 " pdb="MG B MG A2802 " model vdw 2.037 2.170 nonbonded pdb=" O1G DGT A2801 " pdb="MG B MG A2802 " model vdw 2.087 2.170 nonbonded pdb=" ND2 ASN A2234 " pdb=" O PHE A2657 " model vdw 2.141 2.520 nonbonded pdb=" NH1 ARG A1989 " pdb=" OE1 GLU A2096 " model vdw 2.259 2.520 ... (remaining 45800 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 3.760 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.600 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 : 0.013 0.344 5382 Z= 0.648 Angle : 0.838 19.588 7385 Z= 0.404 Chirality : 0.045 0.232 845 Planarity : 0.006 0.088 852 Dihedral : 18.603 146.905 2047 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.81 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -0.41 (0.34), residues: 585 helix: 0.71 (0.29), residues: 324 sheet: -0.74 (0.70), residues: 45 loop : -1.66 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A2061 HIS 0.022 0.002 HIS A2286 PHE 0.015 0.002 PHE A2451 TYR 0.019 0.002 TYR A2668 ARG 0.007 0.001 ARG A2245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.600 Fit side-chains REVERT: A 2684 ARG cc_start: 0.7200 (mtm110) cc_final: 0.6928 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 1.6219 time to fit residues: 104.0935 Evaluate side-chains 52 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.0770 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5382 Z= 0.171 Angle : 0.532 5.678 7385 Z= 0.287 Chirality : 0.040 0.157 845 Planarity : 0.005 0.065 852 Dihedral : 18.059 136.678 904 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.30 % Favored : 94.53 % Rotamer: Outliers : 0.77 % Allowed : 6.37 % Favored : 92.86 % 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: 0.07 (0.35), residues: 585 helix: 1.21 (0.29), residues: 329 sheet: -0.54 (0.67), residues: 49 loop : -1.72 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A2061 HIS 0.011 0.001 HIS A2286 PHE 0.011 0.001 PHE A2451 TYR 0.013 0.001 TYR A2668 ARG 0.007 0.000 ARG A2654 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.592 Fit side-chains REVERT: A 2244 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.7005 (mp0) outliers start: 4 outliers final: 0 residues processed: 64 average time/residue: 1.5007 time to fit residues: 99.6245 Evaluate side-chains 55 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2244 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5382 Z= 0.246 Angle : 0.580 6.458 7385 Z= 0.311 Chirality : 0.042 0.173 845 Planarity : 0.005 0.058 852 Dihedral : 18.173 132.537 904 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.16 % Allowed : 8.30 % Favored : 90.54 % 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: 0.07 (0.35), residues: 585 helix: 1.19 (0.28), residues: 328 sheet: -0.46 (0.69), residues: 45 loop : -1.69 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A2061 HIS 0.003 0.001 HIS A2286 PHE 0.017 0.002 PHE A2451 TYR 0.016 0.001 TYR A2668 ARG 0.006 0.001 ARG A2245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.597 Fit side-chains REVERT: A 2244 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: A 2684 ARG cc_start: 0.7153 (mtm110) cc_final: 0.6938 (ptt-90) outliers start: 6 outliers final: 2 residues processed: 62 average time/residue: 1.5509 time to fit residues: 99.6520 Evaluate side-chains 59 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2244 GLU Chi-restraints excluded: chain A residue 2352 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5382 Z= 0.237 Angle : 0.579 7.767 7385 Z= 0.308 Chirality : 0.042 0.175 845 Planarity : 0.004 0.043 852 Dihedral : 18.185 132.568 904 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.93 % Allowed : 10.81 % Favored : 87.26 % 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: 0.12 (0.35), residues: 585 helix: 1.28 (0.29), residues: 328 sheet: -0.45 (0.68), residues: 45 loop : -1.73 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A2061 HIS 0.003 0.001 HIS A2638 PHE 0.016 0.002 PHE A2451 TYR 0.016 0.001 TYR A2668 ARG 0.007 0.001 ARG A2654 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.607 Fit side-chains REVERT: A 2244 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: A 2562 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6640 (tt0) REVERT: A 2673 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6298 (pt0) REVERT: A 2684 ARG cc_start: 0.7209 (mtm110) cc_final: 0.6947 (ptt-90) outliers start: 10 outliers final: 2 residues processed: 63 average time/residue: 1.5770 time to fit residues: 102.9799 Evaluate side-chains 61 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2244 GLU Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2562 GLU Chi-restraints excluded: chain A residue 2673 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.0030 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5382 Z= 0.229 Angle : 0.576 8.747 7385 Z= 0.307 Chirality : 0.042 0.180 845 Planarity : 0.004 0.043 852 Dihedral : 18.220 131.812 904 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.51 % Allowed : 10.23 % Favored : 87.26 % 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: 0.16 (0.35), residues: 585 helix: 1.31 (0.29), residues: 328 sheet: -0.50 (0.68), residues: 45 loop : -1.70 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A2061 HIS 0.003 0.001 HIS A2362 PHE 0.016 0.002 PHE A2451 TYR 0.016 0.001 TYR A2668 ARG 0.007 0.001 ARG A2654 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.643 Fit side-chains REVERT: A 2244 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: A 2562 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6651 (tt0) REVERT: A 2684 ARG cc_start: 0.7210 (mtm110) cc_final: 0.6948 (ptt-90) outliers start: 13 outliers final: 4 residues processed: 65 average time/residue: 1.5782 time to fit residues: 106.2933 Evaluate side-chains 58 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2244 GLU Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 2562 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5382 Z= 0.253 Angle : 0.592 8.173 7385 Z= 0.315 Chirality : 0.042 0.189 845 Planarity : 0.005 0.046 852 Dihedral : 18.257 132.076 904 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.93 % Allowed : 11.78 % Favored : 86.29 % 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: 0.10 (0.35), residues: 585 helix: 1.26 (0.29), residues: 328 sheet: -0.59 (0.67), residues: 45 loop : -1.71 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A2061 HIS 0.006 0.001 HIS A2286 PHE 0.017 0.002 PHE A2451 TYR 0.017 0.002 TYR A2668 ARG 0.007 0.001 ARG A2245 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.528 Fit side-chains REVERT: A 2244 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: A 2562 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6702 (tt0) REVERT: A 2684 ARG cc_start: 0.7249 (mtm110) cc_final: 0.6966 (ptt-90) outliers start: 10 outliers final: 4 residues processed: 63 average time/residue: 1.5684 time to fit residues: 102.3956 Evaluate side-chains 59 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2195 VAL Chi-restraints excluded: chain A residue 2244 GLU Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 2562 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.0270 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 overall best weight: 0.2638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2600 GLN A2637 GLN ** A2663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5382 Z= 0.155 Angle : 0.502 6.406 7385 Z= 0.270 Chirality : 0.039 0.152 845 Planarity : 0.004 0.036 852 Dihedral : 17.975 129.663 904 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.35 % Allowed : 12.93 % Favored : 85.71 % 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: 0.49 (0.35), residues: 585 helix: 1.66 (0.29), residues: 327 sheet: -0.56 (0.68), residues: 49 loop : -1.66 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A2499 HIS 0.007 0.001 HIS A2286 PHE 0.010 0.001 PHE A2451 TYR 0.010 0.001 TYR A2668 ARG 0.009 0.001 ARG A2654 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.590 Fit side-chains REVERT: A 2210 LYS cc_start: 0.7911 (ttpt) cc_final: 0.7664 (ttpt) REVERT: A 2244 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: A 2286 HIS cc_start: 0.6413 (OUTLIER) cc_final: 0.5892 (m170) REVERT: A 2684 ARG cc_start: 0.7083 (mtm110) cc_final: 0.6855 (ptt-90) outliers start: 7 outliers final: 1 residues processed: 66 average time/residue: 1.5664 time to fit residues: 107.0752 Evaluate side-chains 57 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2244 GLU Chi-restraints excluded: chain A residue 2286 HIS Chi-restraints excluded: chain A residue 2352 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.0570 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 chunk 53 optimal weight: 0.4980 chunk 56 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5382 Z= 0.166 Angle : 0.506 6.307 7385 Z= 0.271 Chirality : 0.039 0.139 845 Planarity : 0.004 0.039 852 Dihedral : 17.948 130.919 904 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.35 % Allowed : 13.51 % Favored : 85.14 % 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 (0.35), residues: 585 helix: 1.78 (0.29), residues: 326 sheet: -0.55 (0.69), residues: 49 loop : -1.61 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A2499 HIS 0.007 0.001 HIS A2286 PHE 0.012 0.001 PHE A2451 TYR 0.010 0.001 TYR A2668 ARG 0.009 0.000 ARG A2654 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.576 Fit side-chains REVERT: A 2210 LYS cc_start: 0.7891 (ttpt) cc_final: 0.7654 (ttpt) REVERT: A 2244 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: A 2286 HIS cc_start: 0.6455 (OUTLIER) cc_final: 0.5933 (m170) REVERT: A 2539 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6671 (mm-30) REVERT: A 2562 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6634 (tt0) REVERT: A 2673 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6103 (pt0) REVERT: A 2684 ARG cc_start: 0.7102 (mtm110) cc_final: 0.6870 (ptt-90) outliers start: 7 outliers final: 1 residues processed: 64 average time/residue: 1.7169 time to fit residues: 113.6477 Evaluate side-chains 59 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2244 GLU Chi-restraints excluded: chain A residue 2286 HIS Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2539 GLU Chi-restraints excluded: chain A residue 2562 GLU Chi-restraints excluded: chain A residue 2673 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2600 GLN ** A2663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5382 Z= 0.331 Angle : 0.649 6.566 7385 Z= 0.345 Chirality : 0.045 0.194 845 Planarity : 0.005 0.054 852 Dihedral : 18.276 132.975 904 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.54 % Allowed : 14.29 % Favored : 84.17 % 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: 0.05 (0.34), residues: 585 helix: 1.22 (0.28), residues: 330 sheet: -0.83 (0.65), residues: 45 loop : -1.71 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A2061 HIS 0.007 0.001 HIS A2286 PHE 0.018 0.002 PHE A2451 TYR 0.024 0.002 TYR A2668 ARG 0.009 0.001 ARG A2245 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.640 Fit side-chains REVERT: A 2244 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: A 2286 HIS cc_start: 0.6477 (OUTLIER) cc_final: 0.5936 (m170) REVERT: A 2539 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6615 (mm-30) REVERT: A 2562 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6772 (tt0) REVERT: A 2673 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6304 (pt0) REVERT: A 2684 ARG cc_start: 0.7260 (mtm110) cc_final: 0.6976 (ptt-90) outliers start: 8 outliers final: 1 residues processed: 61 average time/residue: 1.6402 time to fit residues: 103.5873 Evaluate side-chains 59 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2244 GLU Chi-restraints excluded: chain A residue 2286 HIS Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2539 GLU Chi-restraints excluded: chain A residue 2562 GLU Chi-restraints excluded: chain A residue 2673 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.0050 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.4752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5382 Z= 0.188 Angle : 0.536 5.759 7385 Z= 0.287 Chirality : 0.040 0.157 845 Planarity : 0.004 0.040 852 Dihedral : 18.050 131.026 904 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.35 % Allowed : 15.06 % Favored : 83.59 % 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: 0.36 (0.35), residues: 585 helix: 1.52 (0.29), residues: 327 sheet: -0.77 (0.67), residues: 45 loop : -1.61 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A2499 HIS 0.007 0.001 HIS A2286 PHE 0.013 0.001 PHE A2451 TYR 0.014 0.001 TYR A2668 ARG 0.009 0.001 ARG A2654 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.558 Fit side-chains REVERT: A 2244 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: A 2539 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6581 (mm-30) REVERT: A 2562 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6625 (tt0) REVERT: A 2673 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6139 (pt0) REVERT: A 2684 ARG cc_start: 0.7145 (mtm110) cc_final: 0.6884 (ptt-90) outliers start: 7 outliers final: 2 residues processed: 61 average time/residue: 1.5947 time to fit residues: 100.7884 Evaluate side-chains 61 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2069 ILE Chi-restraints excluded: chain A residue 2244 GLU Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2539 GLU Chi-restraints excluded: chain A residue 2562 GLU Chi-restraints excluded: chain A residue 2673 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 41 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.200020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.175500 restraints weight = 4664.404| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.44 r_work: 0.3687 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5382 Z= 0.199 Angle : 0.543 5.952 7385 Z= 0.290 Chirality : 0.040 0.168 845 Planarity : 0.004 0.044 852 Dihedral : 18.016 131.066 904 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.35 % Allowed : 15.25 % Favored : 83.40 % 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: 0.43 (0.35), residues: 585 helix: 1.56 (0.29), residues: 328 sheet: -0.73 (0.68), residues: 45 loop : -1.54 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A2499 HIS 0.010 0.001 HIS A2286 PHE 0.015 0.002 PHE A2451 TYR 0.014 0.001 TYR A2668 ARG 0.008 0.001 ARG A2245 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2324.07 seconds wall clock time: 42 minutes 0.49 seconds (2520.49 seconds total)