Starting phenix.real_space_refine on Tue Feb 13 11:38:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efc_28078/02_2024/8efc_28078_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efc_28078/02_2024/8efc_28078.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efc_28078/02_2024/8efc_28078_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efc_28078/02_2024/8efc_28078_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efc_28078/02_2024/8efc_28078_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efc_28078/02_2024/8efc_28078.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efc_28078/02_2024/8efc_28078.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efc_28078/02_2024/8efc_28078_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efc_28078/02_2024/8efc_28078_updated.pdb" } resolution = 2.8 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= 0.110 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 41 5.49 5 Mg 1 5.21 5 S 28 5.16 5 C 3356 2.51 5 N 970 2.21 5 O 1106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5502 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4690 Classifications: {'peptide': 595} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 571} Chain breaks: 7 Chain: "E" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 408 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} 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: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 372 Unusual residues: {'2DA': 1} Classifications: {'DNA': 18, 'undetermined': 1} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17, 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: 3.64, per 1000 atoms: 0.66 Number of scatterers: 5502 At special positions: 0 Unit cell: (73.14, 96.46, 96.46, 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 41 15.00 Mg 1 11.99 O 1106 8.00 N 970 7.00 C 3356 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: 3.04 Conformation dependent library (CDL) restraints added in 968.8 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1122 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 5 sheets defined 49.4% alpha, 7.7% beta 16 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 1989 through 1999 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 2164 Processing helix chain 'A' and resid 2169 through 2175 Proline residue: A2173 - end of helix Processing helix chain 'A' and resid 2186 through 2211 removed outlier: 3.685A pdb=" N ALA A2191 " --> pdb=" O ARG A2187 " (cutoff:3.500A) removed outlier: 3.502A 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 2334 through 2350 Processing helix chain 'A' and resid 2352 through 2358 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 2586 No H-bonds generated for 'chain 'A' and resid 2584 through 2586' 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 2116 through 2118 Processing sheet with id= B, first strand: chain 'A' and resid 2236 through 2238 removed outlier: 3.835A pdb=" N ASP A2368 " --> pdb=" O PHE A2238 " (cutoff:3.500A) 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 230 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 2.71 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: 1266 1.33 - 1.45: 1264 1.45 - 1.57: 3027 1.57 - 1.69: 79 1.69 - 1.81: 41 Bond restraints: 5677 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 2.96e+02 bond pdb=" C4' 2DA F 20 " pdb=" O4' 2DA F 20 " ideal model delta sigma weight residual 1.288 1.615 -0.327 2.00e-02 2.50e+03 2.68e+02 bond pdb=" C3' 2DA F 20 " pdb=" C2' 2DA F 20 " ideal model delta sigma weight residual 1.271 1.525 -0.254 2.00e-02 2.50e+03 1.62e+02 bond pdb=" O4' 2DA F 20 " pdb=" C1' 2DA F 20 " ideal model delta sigma weight residual 1.525 1.281 0.244 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 1.514 -0.230 2.00e-02 2.50e+03 1.32e+02 ... (remaining 5672 not shown) Histogram of bond angle deviations from ideal: 94.78 - 104.79: 215 104.79 - 114.80: 3613 114.80 - 124.82: 3804 124.82 - 134.83: 211 134.83 - 144.84: 1 Bond angle restraints: 7844 Sorted by residual: angle pdb=" O3' DG E 8 " pdb=" C3' DG E 8 " pdb=" C2' DG E 8 " ideal model delta sigma weight residual 111.50 100.25 11.25 1.50e+00 4.44e-01 5.63e+01 angle pdb=" C ARG A2343 " pdb=" CA ARG A2343 " pdb=" CB ARG A2343 " ideal model delta sigma weight residual 110.90 99.46 11.44 1.58e+00 4.01e-01 5.24e+01 angle pdb=" PA DGT A2801 " pdb=" O3A DGT A2801 " pdb=" PB DGT A2801 " ideal model delta sigma weight residual 123.57 144.84 -21.27 3.00e+00 1.11e-01 5.03e+01 angle pdb=" O ARG A2343 " pdb=" C ARG A2343 " pdb=" N ILE A2344 " ideal model delta sigma weight residual 122.09 128.26 -6.17 1.08e+00 8.57e-01 3.26e+01 angle pdb=" N ARG A2343 " pdb=" CA ARG A2343 " pdb=" CB ARG A2343 " ideal model delta sigma weight residual 110.07 117.40 -7.33 1.45e+00 4.76e-01 2.55e+01 ... (remaining 7839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 3123 34.97 - 69.95: 186 69.95 - 104.92: 2 104.92 - 139.89: 1 139.89 - 174.87: 1 Dihedral angle restraints: 3313 sinusoidal: 1585 harmonic: 1728 Sorted by residual: dihedral pdb=" O1B DGT A2801 " pdb=" O3B DGT A2801 " pdb=" PB DGT A2801 " pdb=" PG DGT A2801 " ideal model delta sinusoidal sigma weight residual 301.68 172.42 129.26 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C4' DG F 9 " pdb=" C3' DG F 9 " pdb=" O3' DG F 9 " pdb=" P DG F 10 " ideal model delta sinusoidal sigma weight residual 220.00 45.13 174.87 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C ARG A2343 " pdb=" N ARG A2343 " pdb=" CA ARG A2343 " pdb=" CB ARG A2343 " ideal model delta harmonic sigma weight residual -122.60 -113.51 -9.09 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 3310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 636 0.035 - 0.069: 191 0.069 - 0.104: 52 0.104 - 0.139: 14 0.139 - 0.174: 5 Chirality restraints: 898 Sorted by residual: chirality pdb=" CA GLU A2387 " pdb=" N GLU A2387 " pdb=" C GLU A2387 " pdb=" CB GLU A2387 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" C1' 2DA F 20 " pdb=" O4' 2DA F 20 " pdb=" C2' 2DA F 20 " pdb=" N9 2DA F 20 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" C3' DGT A2801 " pdb=" C2' DGT A2801 " pdb=" C4' DGT A2801 " pdb=" O3' DGT A2801 " both_signs ideal model delta sigma weight residual False -2.42 -2.59 0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 895 not shown) Planarity restraints: 860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DGT A2801 " -0.081 2.00e-02 2.50e+03 3.56e-02 3.80e+01 pdb=" C2 DGT A2801 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DGT A2801 " 0.031 2.00e-02 2.50e+03 pdb=" C5 DGT A2801 " 0.017 2.00e-02 2.50e+03 pdb=" C6 DGT A2801 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DGT A2801 " -0.003 2.00e-02 2.50e+03 pdb=" N1 DGT A2801 " -0.038 2.00e-02 2.50e+03 pdb=" N2 DGT A2801 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DGT A2801 " 0.043 2.00e-02 2.50e+03 pdb=" N7 DGT A2801 " 0.020 2.00e-02 2.50e+03 pdb=" N9 DGT A2801 " 0.035 2.00e-02 2.50e+03 pdb=" O6 DGT A2801 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG E 8 " -0.016 2.00e-02 2.50e+03 1.48e-02 6.55e+00 pdb=" N9 DG E 8 " 0.043 2.00e-02 2.50e+03 pdb=" C8 DG E 8 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DG E 8 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DG E 8 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG E 8 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG E 8 " 0.003 2.00e-02 2.50e+03 pdb=" N1 DG E 8 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG E 8 " -0.011 2.00e-02 2.50e+03 pdb=" N2 DG E 8 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DG E 8 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DG E 8 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A2329 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A2330 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A2330 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A2330 " -0.022 5.00e-02 4.00e+02 ... (remaining 857 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 38 2.50 - 3.10: 3888 3.10 - 3.70: 9144 3.70 - 4.30: 13610 4.30 - 4.90: 21281 Nonbonded interactions: 47961 Sorted by model distance: nonbonded pdb=" O2B DGT A2801 " pdb="MG B MG A2802 " model vdw 1.900 2.170 nonbonded pdb=" O1G DGT A2801 " pdb="MG B MG A2802 " model vdw 1.908 2.170 nonbonded pdb=" OE1 GLU A2468 " pdb=" OH TYR A2524 " model vdw 2.140 2.440 nonbonded pdb=" OD2 ASP A2463 " pdb="MG B MG A2802 " model vdw 2.177 2.170 nonbonded pdb=" N4 DC E 25 " pdb=" O6 DG F 5 " model vdw 2.264 2.520 ... (remaining 47956 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 3.730 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.590 Find NCS groups from input model: 0.160 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:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 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 0.344 5677 Z= 0.580 Angle : 0.813 21.272 7844 Z= 0.392 Chirality : 0.039 0.174 898 Planarity : 0.004 0.039 860 Dihedral : 18.187 174.868 2191 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.01 % Favored : 94.65 % Rotamer: Outliers : 1.16 % Allowed : 3.29 % Favored : 95.54 % Cbeta Deviations : 0.18 % 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: -0.15 (0.36), residues: 579 helix: 1.02 (0.29), residues: 329 sheet: -1.31 (0.67), residues: 58 loop : -1.63 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A2341 HIS 0.003 0.001 HIS A2474 PHE 0.011 0.001 PHE A2397 TYR 0.013 0.001 TYR A2668 ARG 0.009 0.000 ARG A2343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.557 Fit side-chains REVERT: A 2201 MET cc_start: 0.7115 (tpt) cc_final: 0.6768 (tpt) REVERT: A 2463 ASP cc_start: 0.6866 (t70) cc_final: 0.6511 (t0) REVERT: A 2553 TYR cc_start: 0.7147 (m-80) cc_final: 0.6899 (m-80) REVERT: A 2577 MET cc_start: 0.6636 (mtp) cc_final: 0.6272 (mtp) REVERT: A 2626 ARG cc_start: 0.7359 (mmm160) cc_final: 0.7056 (mmm160) REVERT: A 2665 GLU cc_start: 0.6556 (tt0) cc_final: 0.6341 (tt0) outliers start: 6 outliers final: 3 residues processed: 87 average time/residue: 1.0167 time to fit residues: 93.2713 Evaluate side-chains 66 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2059 VAL Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2676 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** A2508 ASN ** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5677 Z= 0.227 Angle : 0.603 9.198 7844 Z= 0.307 Chirality : 0.040 0.171 898 Planarity : 0.004 0.036 860 Dihedral : 21.834 172.696 1055 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.53 % Favored : 94.13 % Rotamer: Outliers : 1.16 % Allowed : 8.72 % Favored : 90.12 % 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: 0.00 (0.36), residues: 579 helix: 1.14 (0.29), residues: 328 sheet: -1.46 (0.62), residues: 64 loop : -1.44 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A2341 HIS 0.003 0.001 HIS A2474 PHE 0.013 0.001 PHE A2397 TYR 0.016 0.001 TYR A2668 ARG 0.005 0.000 ARG A2102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.568 Fit side-chains REVERT: A 2156 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6237 (pp20) REVERT: A 2201 MET cc_start: 0.7253 (tpt) cc_final: 0.6594 (mmm) REVERT: A 2553 TYR cc_start: 0.7283 (m-80) cc_final: 0.7062 (m-80) REVERT: A 2577 MET cc_start: 0.6773 (mtp) cc_final: 0.6387 (mtp) REVERT: A 2626 ARG cc_start: 0.7342 (mmm160) cc_final: 0.7011 (mmm160) outliers start: 6 outliers final: 2 residues processed: 69 average time/residue: 0.9521 time to fit residues: 69.6512 Evaluate side-chains 62 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2133 CYS Chi-restraints excluded: chain A residue 2156 GLU Chi-restraints excluded: chain A residue 2602 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** A2479 GLN ** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5677 Z= 0.219 Angle : 0.590 9.471 7844 Z= 0.299 Chirality : 0.039 0.157 898 Planarity : 0.004 0.031 860 Dihedral : 21.761 172.880 1052 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.70 % Favored : 93.96 % Rotamer: Outliers : 1.74 % Allowed : 10.47 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.36), residues: 579 helix: 1.29 (0.29), residues: 325 sheet: -1.44 (0.62), residues: 64 loop : -1.42 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A2706 HIS 0.003 0.001 HIS A2474 PHE 0.013 0.001 PHE A2397 TYR 0.015 0.001 TYR A2668 ARG 0.005 0.000 ARG A2102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.592 Fit side-chains REVERT: A 2201 MET cc_start: 0.7311 (tpt) cc_final: 0.6156 (tpt) REVERT: A 2463 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7010 (t70) REVERT: A 2577 MET cc_start: 0.6721 (mtp) cc_final: 0.6335 (mtp) REVERT: A 2626 ARG cc_start: 0.7311 (mmm160) cc_final: 0.6830 (mmm160) outliers start: 9 outliers final: 3 residues processed: 67 average time/residue: 1.0530 time to fit residues: 74.4331 Evaluate side-chains 62 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2059 VAL Chi-restraints excluded: chain A residue 2133 CYS Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain A residue 2602 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5677 Z= 0.229 Angle : 0.591 9.700 7844 Z= 0.300 Chirality : 0.039 0.156 898 Planarity : 0.004 0.031 860 Dihedral : 21.729 172.318 1052 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.53 % Favored : 94.13 % Rotamer: Outliers : 2.33 % Allowed : 11.24 % Favored : 86.43 % 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: 0.09 (0.36), residues: 579 helix: 1.26 (0.29), residues: 329 sheet: -1.46 (0.62), residues: 64 loop : -1.51 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A2706 HIS 0.003 0.001 HIS A2474 PHE 0.013 0.001 PHE A2397 TYR 0.016 0.001 TYR A2668 ARG 0.005 0.000 ARG A2102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.585 Fit side-chains REVERT: A 2142 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.5459 (mm-30) REVERT: A 2156 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6266 (pp20) REVERT: A 2201 MET cc_start: 0.7277 (tpt) cc_final: 0.6080 (tpt) outliers start: 12 outliers final: 6 residues processed: 70 average time/residue: 0.9557 time to fit residues: 70.9396 Evaluate side-chains 68 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2059 VAL Chi-restraints excluded: chain A residue 2133 CYS Chi-restraints excluded: chain A residue 2142 GLU Chi-restraints excluded: chain A residue 2156 GLU Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2682 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2389 ASN ** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5677 Z= 0.188 Angle : 0.549 7.874 7844 Z= 0.283 Chirality : 0.038 0.139 898 Planarity : 0.004 0.033 860 Dihedral : 21.558 171.597 1052 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.18 % Favored : 94.65 % Rotamer: Outliers : 2.33 % Allowed : 12.60 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.36), residues: 579 helix: 1.43 (0.29), residues: 330 sheet: -1.10 (0.67), residues: 58 loop : -1.45 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2706 HIS 0.003 0.001 HIS A2474 PHE 0.011 0.001 PHE A2397 TYR 0.013 0.001 TYR A2668 ARG 0.005 0.000 ARG A2102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.572 Fit side-chains REVERT: A 2142 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5553 (mm-30) REVERT: A 2156 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6220 (pp20) REVERT: A 2201 MET cc_start: 0.7338 (tpt) cc_final: 0.6909 (tpt) REVERT: A 2463 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6941 (t70) REVERT: A 2577 MET cc_start: 0.6699 (mtp) cc_final: 0.6163 (mtp) outliers start: 12 outliers final: 4 residues processed: 71 average time/residue: 1.0454 time to fit residues: 78.5763 Evaluate side-chains 68 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2007 LEU Chi-restraints excluded: chain A residue 2059 VAL Chi-restraints excluded: chain A residue 2133 CYS Chi-restraints excluded: chain A residue 2142 GLU Chi-restraints excluded: chain A residue 2156 GLU Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2463 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2389 ASN ** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5677 Z= 0.249 Angle : 0.600 9.331 7844 Z= 0.305 Chirality : 0.040 0.166 898 Planarity : 0.004 0.034 860 Dihedral : 21.620 170.449 1051 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Rotamer: Outliers : 2.52 % Allowed : 13.18 % Favored : 84.30 % 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: 0.11 (0.36), residues: 579 helix: 1.26 (0.29), residues: 330 sheet: -1.53 (0.61), residues: 64 loop : -1.45 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2706 HIS 0.003 0.001 HIS A2377 PHE 0.014 0.002 PHE A2397 TYR 0.017 0.001 TYR A2668 ARG 0.003 0.000 ARG A2382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.559 Fit side-chains REVERT: A 2142 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5684 (mm-30) REVERT: A 2156 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6312 (pp20) REVERT: A 2201 MET cc_start: 0.7213 (tpt) cc_final: 0.5931 (tpt) REVERT: A 2577 MET cc_start: 0.6752 (mtp) cc_final: 0.6231 (mtp) outliers start: 13 outliers final: 8 residues processed: 70 average time/residue: 0.9574 time to fit residues: 71.1427 Evaluate side-chains 69 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2007 LEU Chi-restraints excluded: chain A residue 2059 VAL Chi-restraints excluded: chain A residue 2133 CYS Chi-restraints excluded: chain A residue 2142 GLU Chi-restraints excluded: chain A residue 2156 GLU Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2676 ILE Chi-restraints excluded: chain A residue 2682 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5677 Z= 0.217 Angle : 0.584 10.982 7844 Z= 0.296 Chirality : 0.040 0.208 898 Planarity : 0.004 0.034 860 Dihedral : 21.494 169.796 1051 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Rotamer: Outliers : 2.13 % Allowed : 13.76 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.36), residues: 579 helix: 1.30 (0.29), residues: 330 sheet: -1.21 (0.65), residues: 58 loop : -1.50 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2706 HIS 0.003 0.001 HIS A2474 PHE 0.012 0.001 PHE A2397 TYR 0.015 0.001 TYR A2668 ARG 0.002 0.000 ARG A2102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.521 Fit side-chains REVERT: A 2142 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5702 (mm-30) REVERT: A 2156 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6233 (pp20) REVERT: A 2463 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7160 (t70) REVERT: A 2577 MET cc_start: 0.6741 (mtp) cc_final: 0.6212 (mtp) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 1.0156 time to fit residues: 75.1235 Evaluate side-chains 69 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2007 LEU Chi-restraints excluded: chain A residue 2059 VAL Chi-restraints excluded: chain A residue 2133 CYS Chi-restraints excluded: chain A residue 2142 GLU Chi-restraints excluded: chain A residue 2156 GLU Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2676 ILE Chi-restraints excluded: chain A residue 2682 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2389 ASN ** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5677 Z= 0.255 Angle : 0.600 7.941 7844 Z= 0.308 Chirality : 0.041 0.303 898 Planarity : 0.004 0.034 860 Dihedral : 21.522 168.804 1051 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.96 % Rotamer: Outliers : 2.52 % Allowed : 14.15 % Favored : 83.33 % 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: 0.02 (0.36), residues: 579 helix: 1.18 (0.29), residues: 331 sheet: -1.51 (0.61), residues: 64 loop : -1.50 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2706 HIS 0.003 0.001 HIS A2377 PHE 0.014 0.002 PHE A2397 TYR 0.017 0.001 TYR A2668 ARG 0.002 0.000 ARG A2552 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.604 Fit side-chains REVERT: A 2142 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.5705 (mm-30) REVERT: A 2156 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6319 (pp20) REVERT: A 2577 MET cc_start: 0.6709 (mtp) cc_final: 0.6197 (mtp) outliers start: 13 outliers final: 8 residues processed: 68 average time/residue: 0.9887 time to fit residues: 71.1807 Evaluate side-chains 68 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2007 LEU Chi-restraints excluded: chain A residue 2059 VAL Chi-restraints excluded: chain A residue 2133 CYS Chi-restraints excluded: chain A residue 2142 GLU Chi-restraints excluded: chain A residue 2156 GLU Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2676 ILE Chi-restraints excluded: chain A residue 2682 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 0.0870 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2389 ASN ** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5677 Z= 0.245 Angle : 0.614 11.408 7844 Z= 0.310 Chirality : 0.041 0.238 898 Planarity : 0.004 0.035 860 Dihedral : 21.486 168.319 1051 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.53 % Favored : 94.30 % Rotamer: Outliers : 1.94 % Allowed : 14.73 % Favored : 83.33 % 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: -0.03 (0.36), residues: 579 helix: 1.12 (0.29), residues: 330 sheet: -1.47 (0.61), residues: 64 loop : -1.50 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2706 HIS 0.003 0.001 HIS A2474 PHE 0.013 0.002 PHE A2397 TYR 0.016 0.001 TYR A2668 ARG 0.003 0.000 ARG A2580 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.579 Fit side-chains REVERT: A 2142 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5699 (mm-30) REVERT: A 2156 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6313 (pp20) REVERT: A 2213 MET cc_start: 0.7852 (mtt) cc_final: 0.7292 (mtt) REVERT: A 2577 MET cc_start: 0.6702 (mtp) cc_final: 0.6163 (mtp) outliers start: 10 outliers final: 7 residues processed: 65 average time/residue: 0.9574 time to fit residues: 65.9737 Evaluate side-chains 65 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2007 LEU Chi-restraints excluded: chain A residue 2059 VAL Chi-restraints excluded: chain A residue 2133 CYS Chi-restraints excluded: chain A residue 2142 GLU Chi-restraints excluded: chain A residue 2156 GLU Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2682 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2389 ASN ** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 5677 Z= 0.233 Angle : 0.597 8.005 7844 Z= 0.306 Chirality : 0.041 0.304 898 Planarity : 0.004 0.035 860 Dihedral : 21.412 167.573 1051 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.35 % Favored : 94.47 % Rotamer: Outliers : 1.94 % Allowed : 15.12 % Favored : 82.95 % 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: 0.03 (0.36), residues: 579 helix: 1.16 (0.29), residues: 330 sheet: -1.45 (0.62), residues: 64 loop : -1.47 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2706 HIS 0.003 0.001 HIS A2474 PHE 0.013 0.001 PHE A2397 TYR 0.016 0.001 TYR A2668 ARG 0.003 0.000 ARG A2580 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.521 Fit side-chains REVERT: A 2142 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.5362 (mm-30) REVERT: A 2156 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6299 (pp20) REVERT: A 2201 MET cc_start: 0.6792 (tpt) cc_final: 0.6080 (tpt) REVERT: A 2577 MET cc_start: 0.6701 (mtp) cc_final: 0.6188 (mtp) outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 0.9570 time to fit residues: 64.9242 Evaluate side-chains 65 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2007 LEU Chi-restraints excluded: chain A residue 2059 VAL Chi-restraints excluded: chain A residue 2133 CYS Chi-restraints excluded: chain A residue 2142 GLU Chi-restraints excluded: chain A residue 2156 GLU Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2463 ASP Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2682 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2389 ASN ** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.230229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.207478 restraints weight = 4946.964| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 1.17 r_work: 0.4048 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4061 r_free = 0.4061 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5677 Z= 0.221 Angle : 0.606 11.996 7844 Z= 0.306 Chirality : 0.041 0.291 898 Planarity : 0.004 0.034 860 Dihedral : 21.381 167.045 1051 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.35 % Favored : 94.47 % Rotamer: Outliers : 1.55 % Allowed : 15.70 % Favored : 82.75 % 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: 0.08 (0.36), residues: 579 helix: 1.17 (0.29), residues: 330 sheet: -1.13 (0.66), residues: 58 loop : -1.51 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2706 HIS 0.003 0.001 HIS A2663 PHE 0.012 0.001 PHE A2397 TYR 0.015 0.001 TYR A2668 ARG 0.003 0.000 ARG A2580 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.51 seconds wall clock time: 36 minutes 15.89 seconds (2175.89 seconds total)