Starting phenix.real_space_refine on Wed Feb 12 07:42:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oag_12776/02_2025/7oag_12776.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oag_12776/02_2025/7oag_12776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oag_12776/02_2025/7oag_12776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oag_12776/02_2025/7oag_12776.map" model { file = "/net/cci-nas-00/data/ceres_data/7oag_12776/02_2025/7oag_12776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oag_12776/02_2025/7oag_12776.cif" } resolution = 3.4 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 175 5.16 5 C 4750 2.51 5 N 1325 2.21 5 O 1350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7600 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X Time building chain proxies: 2.64, per 1000 atoms: 0.35 Number of scatterers: 7600 At special positions: 0 Unit cell: (76.911, 76.911, 124.877, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 175 16.00 O 1350 8.00 N 1325 7.00 C 4750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 37 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 39 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.0 seconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 25 sheets defined 47.5% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 13 through 21 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 13 through 21 Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 13 through 21 Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 13 through 21 Processing helix chain 'G' and resid 31 through 35 Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 13 through 21 Processing helix chain 'H' and resid 31 through 35 Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 13 through 21 Processing helix chain 'I' and resid 31 through 35 Processing helix chain 'J' and resid 5 through 9 Processing helix chain 'J' and resid 13 through 21 Processing helix chain 'J' and resid 31 through 35 Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 13 through 21 Processing helix chain 'K' and resid 31 through 35 Processing helix chain 'L' and resid 5 through 9 Processing helix chain 'L' and resid 13 through 21 Processing helix chain 'L' and resid 31 through 35 Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 13 through 21 Processing helix chain 'M' and resid 31 through 35 Processing helix chain 'N' and resid 5 through 9 Processing helix chain 'N' and resid 13 through 21 Processing helix chain 'N' and resid 31 through 35 Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 13 through 21 Processing helix chain 'O' and resid 31 through 35 Processing helix chain 'P' and resid 5 through 9 Processing helix chain 'P' and resid 13 through 21 Processing helix chain 'P' and resid 31 through 35 Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 13 through 21 Processing helix chain 'Q' and resid 31 through 35 Processing helix chain 'R' and resid 5 through 9 Processing helix chain 'R' and resid 13 through 21 Processing helix chain 'R' and resid 31 through 35 Processing helix chain 'S' and resid 5 through 9 Processing helix chain 'S' and resid 13 through 21 Processing helix chain 'S' and resid 31 through 35 Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 13 through 21 Processing helix chain 'T' and resid 31 through 35 Processing helix chain 'U' and resid 5 through 9 Processing helix chain 'U' and resid 13 through 21 Processing helix chain 'U' and resid 31 through 35 Processing helix chain 'V' and resid 5 through 9 Processing helix chain 'V' and resid 13 through 21 Processing helix chain 'V' and resid 31 through 35 Processing helix chain 'W' and resid 5 through 9 Processing helix chain 'W' and resid 13 through 21 Processing helix chain 'W' and resid 31 through 35 Processing helix chain 'X' and resid 5 through 9 Processing helix chain 'X' and resid 13 through 21 Processing helix chain 'X' and resid 31 through 35 Processing helix chain 'Y' and resid 5 through 9 Processing helix chain 'Y' and resid 13 through 21 Processing helix chain 'Y' and resid 31 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AA3, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AA4, first strand: chain 'D' and resid 28 through 30 Processing sheet with id=AA5, first strand: chain 'E' and resid 28 through 30 Processing sheet with id=AA6, first strand: chain 'F' and resid 28 through 30 Processing sheet with id=AA7, first strand: chain 'G' and resid 28 through 30 Processing sheet with id=AA8, first strand: chain 'H' and resid 28 through 30 Processing sheet with id=AA9, first strand: chain 'I' and resid 28 through 30 Processing sheet with id=AB1, first strand: chain 'J' and resid 28 through 30 Processing sheet with id=AB2, first strand: chain 'K' and resid 28 through 30 Processing sheet with id=AB3, first strand: chain 'L' and resid 28 through 30 Processing sheet with id=AB4, first strand: chain 'M' and resid 28 through 30 Processing sheet with id=AB5, first strand: chain 'N' and resid 28 through 30 Processing sheet with id=AB6, first strand: chain 'O' and resid 28 through 30 Processing sheet with id=AB7, first strand: chain 'P' and resid 28 through 30 Processing sheet with id=AB8, first strand: chain 'Q' and resid 28 through 30 Processing sheet with id=AB9, first strand: chain 'R' and resid 28 through 30 Processing sheet with id=AC1, first strand: chain 'S' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'T' and resid 28 through 30 Processing sheet with id=AC3, first strand: chain 'U' and resid 28 through 30 Processing sheet with id=AC4, first strand: chain 'V' and resid 28 through 30 Processing sheet with id=AC5, first strand: chain 'W' and resid 28 through 30 Processing sheet with id=AC6, first strand: chain 'X' and resid 28 through 30 Processing sheet with id=AC7, first strand: chain 'Y' and resid 28 through 30 250 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2350 1.34 - 1.46: 2020 1.46 - 1.57: 3255 1.57 - 1.69: 0 1.69 - 1.80: 200 Bond restraints: 7825 Sorted by residual: bond pdb=" CB TRP V 8 " pdb=" CG TRP V 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.50e+00 bond pdb=" CB TRP P 8 " pdb=" CG TRP P 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.50e+00 bond pdb=" CB TRP M 8 " pdb=" CG TRP M 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.49e+00 bond pdb=" CB TRP R 8 " pdb=" CG TRP R 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.49e+00 bond pdb=" CB TRP J 8 " pdb=" CG TRP J 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.49e+00 ... (remaining 7820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.74: 8591 0.74 - 1.48: 1283 1.48 - 2.22: 351 2.22 - 2.97: 100 2.97 - 3.71: 50 Bond angle restraints: 10375 Sorted by residual: angle pdb=" CA LYS U 26 " pdb=" CB LYS U 26 " pdb=" CG LYS U 26 " ideal model delta sigma weight residual 114.10 117.63 -3.53 2.00e+00 2.50e-01 3.11e+00 angle pdb=" C LEU Q 36 " pdb=" N CYS Q 37 " pdb=" CA CYS Q 37 " ideal model delta sigma weight residual 122.17 119.31 2.86 1.62e+00 3.81e-01 3.11e+00 angle pdb=" CA LYS B 26 " pdb=" CB LYS B 26 " pdb=" CG LYS B 26 " ideal model delta sigma weight residual 114.10 117.62 -3.52 2.00e+00 2.50e-01 3.10e+00 angle pdb=" CA LYS F 26 " pdb=" CB LYS F 26 " pdb=" CG LYS F 26 " ideal model delta sigma weight residual 114.10 117.62 -3.52 2.00e+00 2.50e-01 3.09e+00 angle pdb=" CA LYS G 26 " pdb=" CB LYS G 26 " pdb=" CG LYS G 26 " ideal model delta sigma weight residual 114.10 117.62 -3.52 2.00e+00 2.50e-01 3.09e+00 ... (remaining 10370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.36: 3521 8.36 - 16.72: 633 16.72 - 25.08: 175 25.08 - 33.44: 52 33.44 - 41.80: 28 Dihedral angle restraints: 4409 sinusoidal: 1759 harmonic: 2650 Sorted by residual: dihedral pdb=" CA ILE N 22 " pdb=" CB ILE N 22 " pdb=" CG1 ILE N 22 " pdb=" CD1 ILE N 22 " ideal model delta sinusoidal sigma weight residual 60.00 98.05 -38.05 3 1.50e+01 4.44e-03 6.68e+00 dihedral pdb=" CA ILE W 22 " pdb=" CB ILE W 22 " pdb=" CG1 ILE W 22 " pdb=" CD1 ILE W 22 " ideal model delta sinusoidal sigma weight residual 60.00 98.04 -38.04 3 1.50e+01 4.44e-03 6.68e+00 dihedral pdb=" CA ILE U 22 " pdb=" CB ILE U 22 " pdb=" CG1 ILE U 22 " pdb=" CD1 ILE U 22 " ideal model delta sinusoidal sigma weight residual 60.00 98.03 -38.03 3 1.50e+01 4.44e-03 6.68e+00 ... (remaining 4406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 463 0.025 - 0.049: 148 0.049 - 0.074: 89 0.074 - 0.098: 95 0.098 - 0.123: 55 Chirality restraints: 850 Sorted by residual: chirality pdb=" CA LYS K 26 " pdb=" N LYS K 26 " pdb=" C LYS K 26 " pdb=" CB LYS K 26 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA LYS N 26 " pdb=" N LYS N 26 " pdb=" C LYS N 26 " pdb=" CB LYS N 26 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA LYS L 26 " pdb=" N LYS L 26 " pdb=" C LYS L 26 " pdb=" CB LYS L 26 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 847 not shown) Planarity restraints: 1350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 6 " 0.015 5.00e-02 4.00e+02 2.30e-02 8.49e-01 pdb=" N PRO C 7 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Q 6 " 0.015 5.00e-02 4.00e+02 2.30e-02 8.49e-01 pdb=" N PRO Q 7 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO Q 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO Q 7 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 6 " 0.015 5.00e-02 4.00e+02 2.30e-02 8.48e-01 pdb=" N PRO H 7 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO H 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO H 7 " 0.013 5.00e-02 4.00e+02 ... (remaining 1347 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 178 2.60 - 3.17: 7348 3.17 - 3.75: 12990 3.75 - 4.32: 18358 4.32 - 4.90: 27614 Nonbonded interactions: 66488 Sorted by model distance: nonbonded pdb=" SG CYS M 19 " pdb=" SG CYS M 39 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS B 19 " pdb=" SG CYS B 39 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS E 19 " pdb=" SG CYS E 39 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS Y 19 " pdb=" SG CYS Y 39 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS I 19 " pdb=" SG CYS I 39 " model vdw 2.025 3.760 ... (remaining 66483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.510 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 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 : 0.007 0.038 7825 Z= 0.447 Angle : 0.673 3.707 10375 Z= 0.381 Chirality : 0.049 0.123 850 Planarity : 0.004 0.023 1350 Dihedral : 10.390 38.045 2800 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.28), residues: 950 helix: 1.41 (0.37), residues: 200 sheet: None (None), residues: 0 loop : -0.74 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP R 8 HIS 0.002 0.001 HIS U 16 PHE 0.008 0.001 PHE W 2 TYR 0.005 0.001 TYR F 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.167 Fit side-chains REVERT: L 23 LYS cc_start: 0.9235 (mppt) cc_final: 0.9034 (mmtm) REVERT: L 25 TYR cc_start: 0.9451 (m-80) cc_final: 0.9073 (m-80) REVERT: V 5 ASN cc_start: 0.9346 (t0) cc_final: 0.9021 (t0) REVERT: V 32 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8150 (ttpt) REVERT: X 5 ASN cc_start: 0.9226 (t0) cc_final: 0.8941 (t0) REVERT: X 32 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8137 (mtpt) REVERT: Y 5 ASN cc_start: 0.8722 (t0) cc_final: 0.8509 (t0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.4392 time to fit residues: 62.9406 Evaluate side-chains 104 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 chunk 90 optimal weight: 7.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS C 18 HIS D 18 HIS E 18 HIS F 18 HIS G 18 HIS H 18 HIS I 18 HIS J 18 HIS K 18 HIS L 18 HIS M 18 HIS N 18 HIS O 18 HIS P 18 HIS Q 18 HIS R 18 HIS S 18 HIS T 18 HIS U 18 HIS V 18 HIS W 18 HIS X 18 HIS Y 18 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.038604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.023842 restraints weight = 39248.836| |-----------------------------------------------------------------------------| r_work (start): 0.2417 rms_B_bonded: 5.35 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7825 Z= 0.145 Angle : 0.603 5.130 10375 Z= 0.322 Chirality : 0.046 0.114 850 Planarity : 0.003 0.024 1350 Dihedral : 4.016 23.607 1075 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % 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: -0.46 (0.26), residues: 950 helix: 1.10 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -0.82 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 8 HIS 0.002 0.001 HIS L 18 PHE 0.011 0.001 PHE Y 35 TYR 0.006 0.001 TYR J 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.937 Fit side-chains REVERT: C 26 LYS cc_start: 0.9370 (ptmm) cc_final: 0.9045 (ptmm) REVERT: E 20 LYS cc_start: 0.9536 (mmmt) cc_final: 0.9227 (mmmm) REVERT: F 32 LYS cc_start: 0.9548 (mmtt) cc_final: 0.9342 (mmmt) REVERT: K 5 ASN cc_start: 0.9181 (t0) cc_final: 0.8562 (t0) REVERT: K 13 MET cc_start: 0.8053 (mpp) cc_final: 0.7667 (mpp) REVERT: L 25 TYR cc_start: 0.9369 (m-80) cc_final: 0.9077 (m-80) REVERT: N 25 TYR cc_start: 0.9365 (m-80) cc_final: 0.9000 (m-80) REVERT: O 20 LYS cc_start: 0.9595 (mmmt) cc_final: 0.9255 (mmmm) REVERT: P 5 ASN cc_start: 0.9422 (t0) cc_final: 0.8812 (t0) REVERT: P 20 LYS cc_start: 0.9593 (mmmt) cc_final: 0.9251 (mmmm) REVERT: R 5 ASN cc_start: 0.9387 (t0) cc_final: 0.8839 (t0) REVERT: T 5 ASN cc_start: 0.9311 (t0) cc_final: 0.8760 (t0) REVERT: V 5 ASN cc_start: 0.9251 (t0) cc_final: 0.8674 (t0) REVERT: V 32 LYS cc_start: 0.9284 (mmtt) cc_final: 0.8297 (ttpt) REVERT: X 5 ASN cc_start: 0.9082 (t0) cc_final: 0.8483 (t0) REVERT: X 32 LYS cc_start: 0.9213 (mmtt) cc_final: 0.8390 (mtpt) REVERT: Y 5 ASN cc_start: 0.8521 (t0) cc_final: 0.8099 (t0) REVERT: Y 25 TYR cc_start: 0.9528 (m-80) cc_final: 0.8947 (m-80) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.3878 time to fit residues: 67.7740 Evaluate side-chains 123 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 7.9990 chunk 10 optimal weight: 0.0040 chunk 33 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2349 r_free = 0.2349 target = 0.022062 restraints weight = 39446.079| |-----------------------------------------------------------------------------| r_work (start): 0.2313 rms_B_bonded: 5.19 r_work: 0.2173 rms_B_bonded: 5.19 restraints_weight: 2.0000 r_work (final): 0.2173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7825 Z= 0.193 Angle : 0.565 6.468 10375 Z= 0.293 Chirality : 0.044 0.114 850 Planarity : 0.003 0.025 1350 Dihedral : 3.477 18.589 1075 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.26 % Allowed : 8.65 % Favored : 91.10 % 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: -0.65 (0.26), residues: 950 helix: 1.05 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -0.98 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP W 8 HIS 0.002 0.001 HIS A 16 PHE 0.010 0.001 PHE Y 35 TYR 0.013 0.001 TYR J 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 141 time to evaluate : 0.915 Fit side-chains REVERT: C 26 LYS cc_start: 0.9381 (ptmm) cc_final: 0.8972 (ptmm) REVERT: D 5 ASN cc_start: 0.9172 (t0) cc_final: 0.8713 (t0) REVERT: G 5 ASN cc_start: 0.9207 (t0) cc_final: 0.8515 (t0) REVERT: G 11 ASP cc_start: 0.8238 (t0) cc_final: 0.8035 (t0) REVERT: H 10 GLU cc_start: 0.8941 (pm20) cc_final: 0.8675 (pm20) REVERT: I 5 ASN cc_start: 0.9304 (t0) cc_final: 0.8567 (t0) REVERT: K 5 ASN cc_start: 0.9217 (t0) cc_final: 0.8491 (t0) REVERT: M 5 ASN cc_start: 0.9340 (t0) cc_final: 0.8703 (t0) REVERT: M 10 GLU cc_start: 0.8873 (pm20) cc_final: 0.8539 (pm20) REVERT: O 5 ASN cc_start: 0.9340 (t0) cc_final: 0.8697 (t0) REVERT: O 10 GLU cc_start: 0.8886 (pm20) cc_final: 0.8518 (pm20) REVERT: P 5 ASN cc_start: 0.9363 (t0) cc_final: 0.8697 (t0) REVERT: P 20 LYS cc_start: 0.9594 (mmmt) cc_final: 0.9218 (mmmm) REVERT: Q 5 ASN cc_start: 0.9258 (t0) cc_final: 0.8734 (t0) REVERT: R 5 ASN cc_start: 0.9401 (t0) cc_final: 0.8812 (t0) REVERT: S 20 LYS cc_start: 0.9567 (mmmt) cc_final: 0.9367 (mmmm) REVERT: T 5 ASN cc_start: 0.9350 (t0) cc_final: 0.8741 (t0) REVERT: T 20 LYS cc_start: 0.9568 (mmmt) cc_final: 0.9264 (mmmm) REVERT: V 5 ASN cc_start: 0.9327 (t0) cc_final: 0.8723 (t0) REVERT: V 32 LYS cc_start: 0.9638 (mmtt) cc_final: 0.8899 (mtpt) REVERT: W 26 LYS cc_start: 0.9178 (ptmm) cc_final: 0.8865 (ptmm) REVERT: X 5 ASN cc_start: 0.9192 (t0) cc_final: 0.8568 (t0) REVERT: X 32 LYS cc_start: 0.9623 (mmtt) cc_final: 0.8909 (mtpt) REVERT: Y 25 TYR cc_start: 0.9610 (m-80) cc_final: 0.9095 (m-80) outliers start: 2 outliers final: 0 residues processed: 143 average time/residue: 0.3772 time to fit residues: 63.8746 Evaluate side-chains 130 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.035430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.021458 restraints weight = 39408.414| |-----------------------------------------------------------------------------| r_work (start): 0.2281 rms_B_bonded: 5.03 r_work: 0.2139 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7825 Z= 0.268 Angle : 0.588 5.318 10375 Z= 0.300 Chirality : 0.044 0.110 850 Planarity : 0.003 0.026 1350 Dihedral : 3.777 21.737 1075 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.26 % Allowed : 11.23 % Favored : 88.52 % 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: -0.60 (0.27), residues: 950 helix: 1.35 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.05 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP U 8 HIS 0.002 0.001 HIS K 18 PHE 0.009 0.001 PHE Y 35 TYR 0.013 0.001 TYR G 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.912 Fit side-chains REVERT: C 26 LYS cc_start: 0.9434 (ptmm) cc_final: 0.8989 (ptmm) REVERT: D 20 LYS cc_start: 0.9596 (mmmt) cc_final: 0.9340 (mmmm) REVERT: D 25 TYR cc_start: 0.9547 (m-80) cc_final: 0.9302 (m-80) REVERT: G 5 ASN cc_start: 0.9331 (t0) cc_final: 0.8659 (t0) REVERT: G 11 ASP cc_start: 0.8244 (t0) cc_final: 0.7953 (t0) REVERT: G 25 TYR cc_start: 0.9569 (m-80) cc_final: 0.9325 (m-80) REVERT: H 10 GLU cc_start: 0.8950 (pm20) cc_final: 0.8729 (pm20) REVERT: I 5 ASN cc_start: 0.9336 (t0) cc_final: 0.8617 (t0) REVERT: J 20 LYS cc_start: 0.9599 (mmmt) cc_final: 0.9304 (mmmm) REVERT: K 5 ASN cc_start: 0.9311 (t0) cc_final: 0.8630 (t0) REVERT: M 5 ASN cc_start: 0.9362 (t0) cc_final: 0.8720 (t0) REVERT: M 10 GLU cc_start: 0.9041 (pm20) cc_final: 0.8746 (pm20) REVERT: O 5 ASN cc_start: 0.9346 (t0) cc_final: 0.8707 (t0) REVERT: O 10 GLU cc_start: 0.9034 (pm20) cc_final: 0.8723 (pm20) REVERT: O 13 MET cc_start: 0.8834 (mmt) cc_final: 0.8634 (mmp) REVERT: P 5 ASN cc_start: 0.9474 (t0) cc_final: 0.8777 (t0) REVERT: P 20 LYS cc_start: 0.9612 (mmmt) cc_final: 0.9235 (mmmm) REVERT: Q 5 ASN cc_start: 0.9305 (t0) cc_final: 0.8777 (t0) REVERT: Q 25 TYR cc_start: 0.9604 (m-80) cc_final: 0.9370 (m-80) REVERT: R 5 ASN cc_start: 0.9494 (t0) cc_final: 0.8900 (t0) REVERT: T 5 ASN cc_start: 0.9442 (t0) cc_final: 0.8854 (t0) REVERT: T 20 LYS cc_start: 0.9599 (mmmt) cc_final: 0.9294 (mmmm) REVERT: V 5 ASN cc_start: 0.9496 (t0) cc_final: 0.8874 (t0) REVERT: V 10 GLU cc_start: 0.8809 (pm20) cc_final: 0.8414 (pm20) REVERT: V 32 LYS cc_start: 0.9654 (mmtt) cc_final: 0.8899 (mtpt) REVERT: W 26 LYS cc_start: 0.9194 (ptmm) cc_final: 0.8934 (ptmm) REVERT: X 5 ASN cc_start: 0.9333 (t0) cc_final: 0.8750 (t0) REVERT: X 26 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9011 (ptpp) REVERT: X 32 LYS cc_start: 0.9656 (mmtt) cc_final: 0.8792 (ttpt) outliers start: 2 outliers final: 1 residues processed: 136 average time/residue: 0.3650 time to fit residues: 59.0306 Evaluate side-chains 133 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.035175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2313 r_free = 0.2313 target = 0.021347 restraints weight = 39918.888| |-----------------------------------------------------------------------------| r_work (start): 0.2269 rms_B_bonded: 4.96 r_work: 0.2124 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7825 Z= 0.316 Angle : 0.598 5.697 10375 Z= 0.305 Chirality : 0.045 0.110 850 Planarity : 0.004 0.027 1350 Dihedral : 4.198 22.564 1075 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.26 % Allowed : 11.10 % Favored : 88.65 % 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: -0.57 (0.28), residues: 950 helix: 1.69 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.15 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Y 8 HIS 0.003 0.001 HIS Y 18 PHE 0.008 0.001 PHE Y 2 TYR 0.016 0.001 TYR J 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.927 Fit side-chains REVERT: D 20 LYS cc_start: 0.9638 (mmmt) cc_final: 0.9386 (mmmm) REVERT: D 25 TYR cc_start: 0.9584 (m-80) cc_final: 0.9309 (m-80) REVERT: G 11 ASP cc_start: 0.8280 (t0) cc_final: 0.7920 (t0) REVERT: H 10 GLU cc_start: 0.8938 (pm20) cc_final: 0.8676 (pm20) REVERT: J 20 LYS cc_start: 0.9650 (mmmt) cc_final: 0.9380 (mmmm) REVERT: K 5 ASN cc_start: 0.9365 (t0) cc_final: 0.8772 (t0) REVERT: K 10 GLU cc_start: 0.9030 (pm20) cc_final: 0.8708 (pm20) REVERT: M 5 ASN cc_start: 0.9390 (t0) cc_final: 0.8778 (t0) REVERT: M 10 GLU cc_start: 0.9147 (pm20) cc_final: 0.8897 (pm20) REVERT: M 26 LYS cc_start: 0.9504 (ptmt) cc_final: 0.9023 (ptmm) REVERT: O 5 ASN cc_start: 0.9351 (t0) cc_final: 0.8747 (t0) REVERT: O 10 GLU cc_start: 0.9098 (pm20) cc_final: 0.8859 (pm20) REVERT: P 20 LYS cc_start: 0.9645 (mmmt) cc_final: 0.9265 (mmmm) REVERT: R 5 ASN cc_start: 0.9483 (t0) cc_final: 0.8938 (t0) REVERT: T 5 ASN cc_start: 0.9453 (t0) cc_final: 0.8950 (t0) REVERT: T 20 LYS cc_start: 0.9629 (mmmt) cc_final: 0.9323 (mmmm) REVERT: V 5 ASN cc_start: 0.9527 (t0) cc_final: 0.8902 (t0) REVERT: V 32 LYS cc_start: 0.9647 (mmtt) cc_final: 0.8887 (mtpt) REVERT: W 26 LYS cc_start: 0.9228 (ptmm) cc_final: 0.8914 (ptmm) REVERT: X 5 ASN cc_start: 0.9433 (t0) cc_final: 0.8835 (t0) REVERT: X 26 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9016 (ptpp) REVERT: X 32 LYS cc_start: 0.9689 (mmtt) cc_final: 0.8859 (ttpt) REVERT: Y 25 TYR cc_start: 0.9629 (m-80) cc_final: 0.9232 (m-80) REVERT: Y 26 LYS cc_start: 0.9190 (ptmm) cc_final: 0.8916 (ptmm) outliers start: 2 outliers final: 1 residues processed: 131 average time/residue: 0.3732 time to fit residues: 58.1286 Evaluate side-chains 131 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.036181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2348 r_free = 0.2348 target = 0.022000 restraints weight = 39270.749| |-----------------------------------------------------------------------------| r_work (start): 0.2297 rms_B_bonded: 5.06 r_work: 0.2158 rms_B_bonded: 5.02 restraints_weight: 2.0000 r_work (final): 0.2158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 7825 Z= 0.176 Angle : 0.547 6.571 10375 Z= 0.280 Chirality : 0.042 0.109 850 Planarity : 0.003 0.025 1350 Dihedral : 3.774 20.812 1075 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.26 % Allowed : 11.87 % Favored : 87.87 % 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: -0.50 (0.28), residues: 950 helix: 1.85 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.14 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Y 8 HIS 0.002 0.000 HIS L 18 PHE 0.005 0.001 PHE Y 35 TYR 0.016 0.001 TYR F 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 1.185 Fit side-chains REVERT: B 5 ASN cc_start: 0.9242 (t0) cc_final: 0.8821 (t0) REVERT: D 20 LYS cc_start: 0.9631 (mmmt) cc_final: 0.9351 (mmmm) REVERT: G 5 ASN cc_start: 0.9217 (t0) cc_final: 0.8500 (t0) REVERT: G 11 ASP cc_start: 0.8186 (t0) cc_final: 0.7888 (t0) REVERT: G 20 LYS cc_start: 0.9554 (mmmt) cc_final: 0.9351 (mmmm) REVERT: G 25 TYR cc_start: 0.9544 (m-80) cc_final: 0.9257 (m-80) REVERT: H 10 GLU cc_start: 0.8944 (pm20) cc_final: 0.8689 (pm20) REVERT: H 25 TYR cc_start: 0.9460 (m-80) cc_final: 0.9160 (m-80) REVERT: I 5 ASN cc_start: 0.9211 (t0) cc_final: 0.8423 (t0) REVERT: I 10 GLU cc_start: 0.8853 (pm20) cc_final: 0.8623 (pm20) REVERT: J 20 LYS cc_start: 0.9635 (mmmt) cc_final: 0.9332 (mmmm) REVERT: K 5 ASN cc_start: 0.9239 (t0) cc_final: 0.8549 (t0) REVERT: M 5 ASN cc_start: 0.9301 (t0) cc_final: 0.8587 (t0) REVERT: M 26 LYS cc_start: 0.9488 (ptmt) cc_final: 0.8996 (ptmm) REVERT: O 5 ASN cc_start: 0.9248 (t0) cc_final: 0.8587 (t0) REVERT: O 10 GLU cc_start: 0.9082 (pm20) cc_final: 0.8881 (pm20) REVERT: P 5 ASN cc_start: 0.9330 (t0) cc_final: 0.8959 (t0) REVERT: P 20 LYS cc_start: 0.9623 (mmmt) cc_final: 0.9252 (mmmm) REVERT: Q 5 ASN cc_start: 0.9225 (t0) cc_final: 0.8635 (t0) REVERT: Q 20 LYS cc_start: 0.9663 (mmmt) cc_final: 0.9449 (mmmm) REVERT: R 5 ASN cc_start: 0.9357 (t0) cc_final: 0.8896 (t0) REVERT: S 20 LYS cc_start: 0.9649 (mmmt) cc_final: 0.9438 (mmmm) REVERT: T 5 ASN cc_start: 0.9350 (t0) cc_final: 0.8712 (t0) REVERT: T 20 LYS cc_start: 0.9634 (mmmt) cc_final: 0.9321 (mmmm) REVERT: U 20 LYS cc_start: 0.9687 (mmmt) cc_final: 0.9447 (mmmm) REVERT: V 5 ASN cc_start: 0.9420 (t0) cc_final: 0.8750 (t0) REVERT: V 10 GLU cc_start: 0.8733 (pm20) cc_final: 0.8364 (pm20) REVERT: V 32 LYS cc_start: 0.9613 (mmtt) cc_final: 0.8818 (mtpt) REVERT: W 5 ASN cc_start: 0.9272 (t0) cc_final: 0.8669 (t0) REVERT: W 26 LYS cc_start: 0.9231 (ptmm) cc_final: 0.8914 (ptmm) REVERT: X 5 ASN cc_start: 0.9300 (t0) cc_final: 0.8667 (t0) REVERT: X 26 LYS cc_start: 0.9384 (pttm) cc_final: 0.8986 (ptpp) REVERT: X 32 LYS cc_start: 0.9639 (mmtt) cc_final: 0.8912 (mtpt) REVERT: Y 25 TYR cc_start: 0.9645 (m-80) cc_final: 0.9214 (m-80) REVERT: Y 26 LYS cc_start: 0.9173 (ptmm) cc_final: 0.8850 (ptmm) outliers start: 2 outliers final: 0 residues processed: 144 average time/residue: 0.3625 time to fit residues: 62.1289 Evaluate side-chains 139 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 42 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.037207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2402 r_free = 0.2402 target = 0.022957 restraints weight = 38071.017| |-----------------------------------------------------------------------------| r_work (start): 0.2350 rms_B_bonded: 5.05 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7825 Z= 0.140 Angle : 0.540 6.851 10375 Z= 0.274 Chirality : 0.041 0.117 850 Planarity : 0.003 0.024 1350 Dihedral : 3.213 17.944 1075 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % 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: -0.42 (0.27), residues: 950 helix: 2.04 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.13 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP T 8 HIS 0.001 0.000 HIS L 18 PHE 0.003 0.001 PHE P 35 TYR 0.013 0.001 TYR H 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.934 Fit side-chains REVERT: A 5 ASN cc_start: 0.9206 (t0) cc_final: 0.8432 (t0) REVERT: B 5 ASN cc_start: 0.9127 (t0) cc_final: 0.8652 (t0) REVERT: D 5 ASN cc_start: 0.9148 (t0) cc_final: 0.8851 (t0) REVERT: D 20 LYS cc_start: 0.9631 (mmmt) cc_final: 0.9359 (mmmm) REVERT: E 5 ASN cc_start: 0.9139 (t0) cc_final: 0.8408 (t0) REVERT: F 5 ASN cc_start: 0.9185 (t0) cc_final: 0.8711 (t0) REVERT: F 20 LYS cc_start: 0.9587 (mmmt) cc_final: 0.9320 (mmmm) REVERT: G 5 ASN cc_start: 0.9117 (t0) cc_final: 0.8470 (t0) REVERT: G 11 ASP cc_start: 0.8215 (t0) cc_final: 0.7917 (t0) REVERT: G 20 LYS cc_start: 0.9560 (mmmt) cc_final: 0.9273 (mmmm) REVERT: G 25 TYR cc_start: 0.9421 (m-80) cc_final: 0.9080 (m-80) REVERT: H 10 GLU cc_start: 0.8808 (pm20) cc_final: 0.8570 (pm20) REVERT: H 20 LYS cc_start: 0.9595 (mmmt) cc_final: 0.9355 (mmmm) REVERT: H 25 TYR cc_start: 0.9263 (m-80) cc_final: 0.8933 (m-80) REVERT: I 5 ASN cc_start: 0.9061 (t0) cc_final: 0.8348 (t0) REVERT: J 20 LYS cc_start: 0.9675 (mmmt) cc_final: 0.9410 (mmmm) REVERT: K 5 ASN cc_start: 0.9100 (t0) cc_final: 0.8462 (t0) REVERT: K 10 GLU cc_start: 0.8828 (pm20) cc_final: 0.8571 (pm20) REVERT: M 5 ASN cc_start: 0.9112 (t0) cc_final: 0.8456 (t0) REVERT: M 10 GLU cc_start: 0.8937 (pm20) cc_final: 0.8641 (pm20) REVERT: M 26 LYS cc_start: 0.9488 (ptmt) cc_final: 0.9019 (ptmm) REVERT: N 5 ASN cc_start: 0.9267 (t0) cc_final: 0.8985 (t0) REVERT: O 5 ASN cc_start: 0.9092 (t0) cc_final: 0.8447 (t0) REVERT: P 5 ASN cc_start: 0.9239 (t0) cc_final: 0.8937 (t0) REVERT: P 20 LYS cc_start: 0.9628 (mmmt) cc_final: 0.9291 (mmmm) REVERT: Q 5 ASN cc_start: 0.9124 (t0) cc_final: 0.8574 (t0) REVERT: Q 10 GLU cc_start: 0.8955 (pm20) cc_final: 0.8698 (pm20) REVERT: Q 25 TYR cc_start: 0.9473 (m-80) cc_final: 0.9114 (m-80) REVERT: R 5 ASN cc_start: 0.9172 (t0) cc_final: 0.8845 (t0) REVERT: S 5 ASN cc_start: 0.8998 (t0) cc_final: 0.8487 (t0) REVERT: T 5 ASN cc_start: 0.9229 (t0) cc_final: 0.8865 (t0) REVERT: T 20 LYS cc_start: 0.9671 (mmmt) cc_final: 0.9368 (mmmm) REVERT: U 20 LYS cc_start: 0.9674 (mmmt) cc_final: 0.9440 (mmmm) REVERT: V 5 ASN cc_start: 0.9287 (t0) cc_final: 0.8992 (t0) REVERT: V 10 GLU cc_start: 0.8710 (pm20) cc_final: 0.8412 (pm20) REVERT: V 32 LYS cc_start: 0.9474 (mmtt) cc_final: 0.8632 (mtpt) REVERT: W 5 ASN cc_start: 0.9114 (t0) cc_final: 0.8540 (t0) REVERT: W 26 LYS cc_start: 0.9250 (ptmm) cc_final: 0.8927 (ptmm) REVERT: X 5 ASN cc_start: 0.9128 (t0) cc_final: 0.8486 (t0) REVERT: X 26 LYS cc_start: 0.9395 (pttm) cc_final: 0.9038 (ptpp) REVERT: X 32 LYS cc_start: 0.9496 (mmtt) cc_final: 0.8706 (mtpt) REVERT: Y 25 TYR cc_start: 0.9590 (m-80) cc_final: 0.9182 (m-80) REVERT: Y 26 LYS cc_start: 0.9177 (ptmm) cc_final: 0.8827 (ptmm) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.3687 time to fit residues: 68.5312 Evaluate side-chains 146 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.036934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.022561 restraints weight = 38675.167| |-----------------------------------------------------------------------------| r_work (start): 0.2334 rms_B_bonded: 5.09 r_work: 0.2191 rms_B_bonded: 5.08 restraints_weight: 2.0000 r_work (final): 0.2191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7825 Z= 0.158 Angle : 0.567 7.660 10375 Z= 0.285 Chirality : 0.041 0.115 850 Planarity : 0.003 0.024 1350 Dihedral : 3.060 17.974 1075 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % 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: -0.31 (0.28), residues: 950 helix: 2.21 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.09 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP O 8 HIS 0.001 0.000 HIS Q 18 PHE 0.004 0.001 PHE Y 35 TYR 0.014 0.001 TYR U 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.837 Fit side-chains REVERT: A 5 ASN cc_start: 0.9258 (t0) cc_final: 0.8480 (t0) REVERT: B 5 ASN cc_start: 0.9064 (t0) cc_final: 0.8607 (t0) REVERT: D 5 ASN cc_start: 0.9115 (t0) cc_final: 0.8778 (t0) REVERT: D 20 LYS cc_start: 0.9626 (mmmt) cc_final: 0.9423 (mmmm) REVERT: E 5 ASN cc_start: 0.9068 (t0) cc_final: 0.8279 (t0) REVERT: F 5 ASN cc_start: 0.9145 (t0) cc_final: 0.8829 (t0) REVERT: F 20 LYS cc_start: 0.9577 (mmmt) cc_final: 0.9308 (mmmm) REVERT: G 5 ASN cc_start: 0.9042 (t0) cc_final: 0.8327 (t0) REVERT: G 11 ASP cc_start: 0.8173 (t0) cc_final: 0.7889 (t0) REVERT: G 20 LYS cc_start: 0.9543 (mmmt) cc_final: 0.9261 (mmmm) REVERT: G 25 TYR cc_start: 0.9520 (m-80) cc_final: 0.9142 (m-80) REVERT: H 5 ASN cc_start: 0.9151 (t0) cc_final: 0.8826 (t0) REVERT: H 10 GLU cc_start: 0.8954 (pm20) cc_final: 0.8723 (pm20) REVERT: H 20 LYS cc_start: 0.9569 (mmmt) cc_final: 0.9312 (mmmm) REVERT: H 25 TYR cc_start: 0.9427 (m-80) cc_final: 0.8984 (m-80) REVERT: I 5 ASN cc_start: 0.9022 (t0) cc_final: 0.8255 (t0) REVERT: J 20 LYS cc_start: 0.9641 (mmmt) cc_final: 0.9365 (mmmm) REVERT: K 5 ASN cc_start: 0.9087 (t0) cc_final: 0.8422 (t0) REVERT: K 10 GLU cc_start: 0.8955 (pm20) cc_final: 0.8674 (pm20) REVERT: M 5 ASN cc_start: 0.9112 (t0) cc_final: 0.8451 (t0) REVERT: M 10 GLU cc_start: 0.9039 (pm20) cc_final: 0.8753 (pm20) REVERT: M 26 LYS cc_start: 0.9463 (ptmt) cc_final: 0.8946 (ptmm) REVERT: N 5 ASN cc_start: 0.9253 (t0) cc_final: 0.8952 (t0) REVERT: O 5 ASN cc_start: 0.9108 (t0) cc_final: 0.8418 (t0) REVERT: O 10 GLU cc_start: 0.8920 (pm20) cc_final: 0.8570 (pm20) REVERT: P 5 ASN cc_start: 0.9231 (t0) cc_final: 0.8903 (t0) REVERT: P 20 LYS cc_start: 0.9615 (mmmt) cc_final: 0.9239 (mmmm) REVERT: Q 5 ASN cc_start: 0.9065 (t0) cc_final: 0.8476 (t0) REVERT: Q 10 GLU cc_start: 0.9114 (pm20) cc_final: 0.8851 (pm20) REVERT: Q 25 TYR cc_start: 0.9569 (m-80) cc_final: 0.9136 (m-80) REVERT: R 5 ASN cc_start: 0.9242 (t0) cc_final: 0.8917 (t0) REVERT: S 5 ASN cc_start: 0.9034 (t0) cc_final: 0.8499 (t0) REVERT: T 5 ASN cc_start: 0.9192 (t0) cc_final: 0.8891 (t0) REVERT: T 20 LYS cc_start: 0.9633 (mmmt) cc_final: 0.9329 (mmmm) REVERT: U 20 LYS cc_start: 0.9685 (mmmt) cc_final: 0.9425 (mmmm) REVERT: V 5 ASN cc_start: 0.9286 (t0) cc_final: 0.8654 (t0) REVERT: V 10 GLU cc_start: 0.8776 (pm20) cc_final: 0.8417 (pm20) REVERT: V 32 LYS cc_start: 0.9600 (mmtt) cc_final: 0.8792 (mtpt) REVERT: W 5 ASN cc_start: 0.9111 (t0) cc_final: 0.8499 (t0) REVERT: W 26 LYS cc_start: 0.9216 (ptmm) cc_final: 0.8850 (ptmm) REVERT: X 5 ASN cc_start: 0.9162 (t0) cc_final: 0.8550 (t0) REVERT: X 26 LYS cc_start: 0.9356 (pttm) cc_final: 0.8987 (ptpp) REVERT: X 32 LYS cc_start: 0.9611 (mmtt) cc_final: 0.8839 (mtpt) REVERT: Y 5 ASN cc_start: 0.9001 (t0) cc_final: 0.8426 (t0) REVERT: Y 13 MET cc_start: 0.8315 (mmt) cc_final: 0.7935 (mmm) REVERT: Y 25 TYR cc_start: 0.9657 (m-80) cc_final: 0.9213 (m-80) REVERT: Y 26 LYS cc_start: 0.9173 (ptmm) cc_final: 0.8806 (ptmm) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3500 time to fit residues: 64.4522 Evaluate side-chains 151 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.0270 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.037205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2402 r_free = 0.2402 target = 0.022967 restraints weight = 38957.437| |-----------------------------------------------------------------------------| r_work (start): 0.2353 rms_B_bonded: 5.07 r_work (final): 0.2353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7825 Z= 0.156 Angle : 0.590 7.888 10375 Z= 0.295 Chirality : 0.041 0.116 850 Planarity : 0.003 0.023 1350 Dihedral : 2.937 17.913 1075 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.28), residues: 950 helix: 2.28 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.08 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 8 HIS 0.001 0.000 HIS S 18 PHE 0.004 0.000 PHE Y 35 TYR 0.015 0.001 TYR U 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.153 Fit side-chains REVERT: A 5 ASN cc_start: 0.9207 (t0) cc_final: 0.8429 (t0) REVERT: B 5 ASN cc_start: 0.9079 (t0) cc_final: 0.8753 (t0) REVERT: C 5 ASN cc_start: 0.9105 (t0) cc_final: 0.8434 (t0) REVERT: C 10 GLU cc_start: 0.8751 (pm20) cc_final: 0.8460 (pm20) REVERT: D 5 ASN cc_start: 0.9146 (t0) cc_final: 0.8841 (t0) REVERT: D 20 LYS cc_start: 0.9637 (mmmt) cc_final: 0.9372 (mmmm) REVERT: E 5 ASN cc_start: 0.9113 (t0) cc_final: 0.8378 (t0) REVERT: F 5 ASN cc_start: 0.9130 (t0) cc_final: 0.8796 (t0) REVERT: F 20 LYS cc_start: 0.9594 (mmmt) cc_final: 0.9338 (mmmm) REVERT: G 5 ASN cc_start: 0.9084 (t0) cc_final: 0.8425 (t0) REVERT: G 11 ASP cc_start: 0.8194 (t0) cc_final: 0.7902 (t0) REVERT: G 20 LYS cc_start: 0.9568 (mmmt) cc_final: 0.9233 (mmmm) REVERT: G 25 TYR cc_start: 0.9439 (m-80) cc_final: 0.9059 (m-80) REVERT: H 5 ASN cc_start: 0.9176 (t0) cc_final: 0.8901 (t0) REVERT: H 20 LYS cc_start: 0.9614 (mmmt) cc_final: 0.9370 (mmmm) REVERT: H 25 TYR cc_start: 0.9269 (m-80) cc_final: 0.8818 (m-80) REVERT: I 5 ASN cc_start: 0.9035 (t0) cc_final: 0.8317 (t0) REVERT: J 5 ASN cc_start: 0.9208 (t0) cc_final: 0.8874 (t0) REVERT: J 20 LYS cc_start: 0.9664 (mmmt) cc_final: 0.9405 (mmmm) REVERT: K 5 ASN cc_start: 0.9072 (t0) cc_final: 0.8410 (t0) REVERT: K 10 GLU cc_start: 0.8835 (pm20) cc_final: 0.8582 (pm20) REVERT: M 5 ASN cc_start: 0.9069 (t0) cc_final: 0.8411 (t0) REVERT: M 10 GLU cc_start: 0.8923 (pm20) cc_final: 0.8667 (pm20) REVERT: M 26 LYS cc_start: 0.9471 (ptmt) cc_final: 0.8994 (ptmm) REVERT: N 5 ASN cc_start: 0.9224 (t0) cc_final: 0.8967 (t0) REVERT: O 5 ASN cc_start: 0.9031 (t0) cc_final: 0.8405 (t0) REVERT: O 10 GLU cc_start: 0.8832 (pm20) cc_final: 0.8529 (pm20) REVERT: P 5 ASN cc_start: 0.9156 (t0) cc_final: 0.8848 (t0) REVERT: P 20 LYS cc_start: 0.9617 (mmmt) cc_final: 0.9239 (mmmm) REVERT: Q 5 ASN cc_start: 0.9048 (t0) cc_final: 0.8452 (t0) REVERT: Q 10 GLU cc_start: 0.8994 (pm20) cc_final: 0.8765 (pm20) REVERT: Q 22 ILE cc_start: 0.9474 (mp) cc_final: 0.9196 (tp) REVERT: Q 25 TYR cc_start: 0.9475 (m-80) cc_final: 0.8836 (m-80) REVERT: R 5 ASN cc_start: 0.9165 (t0) cc_final: 0.8829 (t0) REVERT: S 5 ASN cc_start: 0.8974 (t0) cc_final: 0.8468 (t0) REVERT: T 5 ASN cc_start: 0.9201 (t0) cc_final: 0.8834 (t0) REVERT: T 10 GLU cc_start: 0.8655 (pm20) cc_final: 0.8335 (pm20) REVERT: T 20 LYS cc_start: 0.9636 (mmmt) cc_final: 0.9348 (mmmm) REVERT: U 5 ASN cc_start: 0.9028 (t0) cc_final: 0.8464 (t0) REVERT: U 20 LYS cc_start: 0.9681 (mmmt) cc_final: 0.9425 (mmmm) REVERT: V 5 ASN cc_start: 0.9233 (t0) cc_final: 0.8611 (t0) REVERT: V 10 GLU cc_start: 0.8727 (pm20) cc_final: 0.8445 (pm20) REVERT: V 32 LYS cc_start: 0.9469 (mmtt) cc_final: 0.8640 (mtpt) REVERT: W 5 ASN cc_start: 0.9086 (t0) cc_final: 0.8508 (t0) REVERT: W 26 LYS cc_start: 0.9245 (ptmm) cc_final: 0.8891 (ptmm) REVERT: X 5 ASN cc_start: 0.9117 (t0) cc_final: 0.8452 (t0) REVERT: X 26 LYS cc_start: 0.9380 (pttm) cc_final: 0.9002 (ptpp) REVERT: X 32 LYS cc_start: 0.9492 (mmtt) cc_final: 0.8706 (mtpt) REVERT: Y 5 ASN cc_start: 0.8932 (t0) cc_final: 0.8381 (t0) REVERT: Y 13 MET cc_start: 0.7915 (mmt) cc_final: 0.7551 (mmm) REVERT: Y 25 TYR cc_start: 0.9591 (m-80) cc_final: 0.9201 (m-80) REVERT: Y 26 LYS cc_start: 0.9178 (ptmm) cc_final: 0.8844 (ptmm) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.3371 time to fit residues: 65.3461 Evaluate side-chains 157 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.035116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2312 r_free = 0.2312 target = 0.021285 restraints weight = 39975.805| |-----------------------------------------------------------------------------| r_work (start): 0.2271 rms_B_bonded: 4.94 r_work: 0.2124 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 7825 Z= 0.382 Angle : 0.713 8.401 10375 Z= 0.354 Chirality : 0.045 0.118 850 Planarity : 0.004 0.024 1350 Dihedral : 3.818 22.578 1075 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 0.00 % Allowed : 12.52 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.29), residues: 950 helix: 2.41 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -1.20 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Y 8 HIS 0.003 0.001 HIS W 18 PHE 0.008 0.001 PHE Q 2 TYR 0.019 0.002 TYR U 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.012 Fit side-chains REVERT: D 20 LYS cc_start: 0.9643 (mmmt) cc_final: 0.9438 (mmmm) REVERT: D 25 TYR cc_start: 0.9605 (m-80) cc_final: 0.9303 (m-80) REVERT: G 5 ASN cc_start: 0.9325 (t0) cc_final: 0.8783 (t0) REVERT: G 11 ASP cc_start: 0.8216 (t0) cc_final: 0.7913 (t0) REVERT: G 20 LYS cc_start: 0.9610 (mmmt) cc_final: 0.9351 (mmmm) REVERT: I 5 ASN cc_start: 0.9348 (t0) cc_final: 0.8643 (t0) REVERT: I 10 GLU cc_start: 0.8951 (pm20) cc_final: 0.8653 (pm20) REVERT: J 20 LYS cc_start: 0.9658 (mmmt) cc_final: 0.9361 (mmmm) REVERT: K 5 ASN cc_start: 0.9359 (t0) cc_final: 0.8725 (t0) REVERT: K 10 GLU cc_start: 0.9008 (pm20) cc_final: 0.8722 (pm20) REVERT: M 5 ASN cc_start: 0.9370 (t0) cc_final: 0.8728 (t0) REVERT: M 10 GLU cc_start: 0.9085 (pm20) cc_final: 0.8800 (pm20) REVERT: M 26 LYS cc_start: 0.9461 (ptmt) cc_final: 0.9018 (ptmm) REVERT: O 5 ASN cc_start: 0.9350 (t0) cc_final: 0.8690 (t0) REVERT: O 10 GLU cc_start: 0.9036 (pm20) cc_final: 0.8708 (pm20) REVERT: P 5 ASN cc_start: 0.9463 (t0) cc_final: 0.8778 (t0) REVERT: P 20 LYS cc_start: 0.9644 (mmmt) cc_final: 0.9282 (mmmm) REVERT: Q 5 ASN cc_start: 0.9303 (t0) cc_final: 0.8712 (t0) REVERT: Q 10 GLU cc_start: 0.9207 (pm20) cc_final: 0.8978 (pm20) REVERT: R 5 ASN cc_start: 0.9489 (t0) cc_final: 0.8831 (t0) REVERT: T 5 ASN cc_start: 0.9437 (t0) cc_final: 0.8819 (t0) REVERT: T 10 GLU cc_start: 0.8908 (pm20) cc_final: 0.8538 (pm20) REVERT: T 20 LYS cc_start: 0.9639 (mmmt) cc_final: 0.9351 (mmmm) REVERT: U 13 MET cc_start: 0.8598 (mmp) cc_final: 0.8383 (mmp) REVERT: V 5 ASN cc_start: 0.9531 (t0) cc_final: 0.8907 (t0) REVERT: V 10 GLU cc_start: 0.8806 (pm20) cc_final: 0.8436 (pm20) REVERT: V 32 LYS cc_start: 0.9654 (mmtt) cc_final: 0.8894 (mtpt) REVERT: W 5 ASN cc_start: 0.9375 (t0) cc_final: 0.8802 (t0) REVERT: W 26 LYS cc_start: 0.9217 (ptmm) cc_final: 0.8861 (ptmm) REVERT: X 5 ASN cc_start: 0.9457 (t0) cc_final: 0.8788 (t0) REVERT: X 26 LYS cc_start: 0.9381 (pttm) cc_final: 0.9010 (ptpp) REVERT: X 32 LYS cc_start: 0.9682 (mmtt) cc_final: 0.8829 (ttpt) REVERT: Y 13 MET cc_start: 0.8202 (mmt) cc_final: 0.7827 (mmm) REVERT: Y 25 TYR cc_start: 0.9641 (m-80) cc_final: 0.9135 (m-80) REVERT: Y 26 LYS cc_start: 0.9173 (ptmm) cc_final: 0.8865 (ptmm) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3582 time to fit residues: 59.7983 Evaluate side-chains 139 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 48 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.037378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.022806 restraints weight = 38486.145| |-----------------------------------------------------------------------------| r_work (start): 0.2318 rms_B_bonded: 5.10 r_work (final): 0.2318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7825 Z= 0.176 Angle : 0.631 8.622 10375 Z= 0.316 Chirality : 0.041 0.114 850 Planarity : 0.003 0.024 1350 Dihedral : 3.693 20.627 1075 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 0.00 % Allowed : 12.90 % Favored : 87.10 % 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 (0.28), residues: 950 helix: 2.29 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.17 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP P 8 HIS 0.002 0.000 HIS T 18 PHE 0.005 0.001 PHE Y 35 TYR 0.016 0.001 TYR H 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3143.75 seconds wall clock time: 58 minutes 7.12 seconds (3487.12 seconds total)