Starting phenix.real_space_refine on Tue Sep 24 08:26:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oag_12776/09_2024/7oag_12776.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oag_12776/09_2024/7oag_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oag_12776/09_2024/7oag_12776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oag_12776/09_2024/7oag_12776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oag_12776/09_2024/7oag_12776.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oag_12776/09_2024/7oag_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-5461/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: 2.56, per 1000 atoms: 0.34 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: 1.87 Conformation dependent library (CDL) restraints added in 1.1 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: 1.15 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: 1.82 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 18.310 Find NCS groups from input model: 0.290 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.908 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: 0.3836 time to fit residues: 54.6934 Evaluate side-chains 104 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 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 fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.905 Fit side-chains REVERT: C 26 LYS cc_start: 0.9404 (ptmm) cc_final: 0.9083 (ptmm) REVERT: E 20 LYS cc_start: 0.9536 (mmmt) cc_final: 0.9222 (mmmm) REVERT: K 5 ASN cc_start: 0.9109 (t0) cc_final: 0.8519 (t0) REVERT: K 13 MET cc_start: 0.7928 (mpp) cc_final: 0.7539 (mpp) REVERT: L 25 TYR cc_start: 0.9340 (m-80) cc_final: 0.9064 (m-80) REVERT: N 25 TYR cc_start: 0.9401 (m-80) cc_final: 0.9037 (m-80) REVERT: O 20 LYS cc_start: 0.9593 (mmmt) cc_final: 0.9258 (mmmm) REVERT: P 5 ASN cc_start: 0.9360 (t0) cc_final: 0.8723 (t0) REVERT: P 20 LYS cc_start: 0.9592 (mmmt) cc_final: 0.9240 (mmmm) REVERT: R 5 ASN cc_start: 0.9332 (t0) cc_final: 0.8788 (t0) REVERT: T 5 ASN cc_start: 0.9179 (t0) cc_final: 0.8675 (t0) REVERT: V 5 ASN cc_start: 0.9126 (t0) cc_final: 0.8640 (t0) REVERT: V 32 LYS cc_start: 0.9254 (mmtt) cc_final: 0.8290 (ttpt) REVERT: X 5 ASN cc_start: 0.8934 (t0) cc_final: 0.8464 (t0) REVERT: X 32 LYS cc_start: 0.9197 (mmtt) cc_final: 0.8402 (mtpt) REVERT: Y 5 ASN cc_start: 0.8509 (t0) cc_final: 0.8183 (t0) REVERT: Y 22 ILE cc_start: 0.9264 (mp) cc_final: 0.9061 (mp) REVERT: Y 25 TYR cc_start: 0.9545 (m-80) cc_final: 0.8944 (m-80) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.3729 time to fit residues: 65.3215 Evaluate side-chains 123 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 7825 Z= 0.470 Angle : 0.703 6.600 10375 Z= 0.361 Chirality : 0.049 0.123 850 Planarity : 0.004 0.027 1350 Dihedral : 4.522 23.036 1075 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.26 % Allowed : 9.29 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 950 helix: 1.13 (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 0.011 0.002 TRP Q 8 HIS 0.003 0.001 HIS Y 18 PHE 0.015 0.002 PHE Y 35 TYR 0.015 0.002 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 118 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.940 Fit side-chains REVERT: C 26 LYS cc_start: 0.9479 (ptmm) cc_final: 0.9204 (ptmm) REVERT: G 11 ASP cc_start: 0.8026 (t0) cc_final: 0.7643 (t0) REVERT: I 11 ASP cc_start: 0.8028 (t0) cc_final: 0.7796 (t0) REVERT: I 13 MET cc_start: 0.8428 (mmm) cc_final: 0.8217 (mmm) REVERT: O 10 GLU cc_start: 0.8886 (pm20) cc_final: 0.8599 (pm20) REVERT: V 5 ASN cc_start: 0.9488 (t0) cc_final: 0.9020 (t0) REVERT: V 32 LYS cc_start: 0.9613 (mmtt) cc_final: 0.8882 (mtpt) REVERT: W 25 TYR cc_start: 0.9493 (m-80) cc_final: 0.9261 (m-80) REVERT: W 26 LYS cc_start: 0.9178 (ptmm) cc_final: 0.8905 (ptmm) REVERT: X 5 ASN cc_start: 0.9401 (t0) cc_final: 0.9067 (t0) REVERT: X 32 LYS cc_start: 0.9628 (mmtt) cc_final: 0.8867 (ttpt) outliers start: 2 outliers final: 1 residues processed: 116 average time/residue: 0.3725 time to fit residues: 51.4104 Evaluate side-chains 112 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7825 Z= 0.156 Angle : 0.533 4.693 10375 Z= 0.277 Chirality : 0.043 0.109 850 Planarity : 0.003 0.025 1350 Dihedral : 3.862 19.819 1075 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 0.26 % Allowed : 10.32 % Favored : 89.42 % 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: -0.66 (0.27), residues: 950 helix: 1.30 (0.34), 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 K 8 HIS 0.001 0.000 HIS R 18 PHE 0.006 0.001 PHE Y 35 TYR 0.015 0.001 TYR F 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 145 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 0.918 Fit side-chains REVERT: B 32 LYS cc_start: 0.9554 (mmtt) cc_final: 0.9330 (mmmt) REVERT: C 26 LYS cc_start: 0.9428 (ptmm) cc_final: 0.9004 (ptmm) REVERT: D 20 LYS cc_start: 0.9606 (mmmt) cc_final: 0.9357 (mmmm) REVERT: G 5 ASN cc_start: 0.9189 (t0) cc_final: 0.8530 (t0) REVERT: G 11 ASP cc_start: 0.8038 (t0) cc_final: 0.7703 (t0) REVERT: I 5 ASN cc_start: 0.9180 (t0) cc_final: 0.8466 (t0) REVERT: I 11 ASP cc_start: 0.7943 (t0) cc_final: 0.7113 (t0) REVERT: I 13 MET cc_start: 0.8234 (mmm) cc_final: 0.7852 (mpp) REVERT: J 20 LYS cc_start: 0.9642 (mmmt) cc_final: 0.9387 (mmmm) REVERT: J 23 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9015 (mtmm) REVERT: K 5 ASN cc_start: 0.9182 (t0) cc_final: 0.8527 (t0) REVERT: K 20 LYS cc_start: 0.9616 (mmmt) cc_final: 0.9411 (mmmm) REVERT: L 20 LYS cc_start: 0.9629 (mmmt) cc_final: 0.9384 (mmmm) REVERT: M 5 ASN cc_start: 0.9220 (t0) cc_final: 0.8584 (t0) REVERT: M 10 GLU cc_start: 0.8836 (pm20) cc_final: 0.8544 (pm20) REVERT: O 5 ASN cc_start: 0.9198 (t0) cc_final: 0.8589 (t0) REVERT: P 5 ASN cc_start: 0.9296 (t0) cc_final: 0.8621 (t0) REVERT: P 20 LYS cc_start: 0.9612 (mmmt) cc_final: 0.9235 (mmmm) REVERT: Q 5 ASN cc_start: 0.9170 (t0) cc_final: 0.8658 (t0) REVERT: Q 25 TYR cc_start: 0.9579 (m-80) cc_final: 0.9307 (m-80) REVERT: R 5 ASN cc_start: 0.9306 (t0) cc_final: 0.8848 (t0) REVERT: S 20 LYS cc_start: 0.9599 (mmmt) cc_final: 0.9397 (mmmm) REVERT: T 5 ASN cc_start: 0.9298 (t0) cc_final: 0.8960 (t0) REVERT: T 20 LYS cc_start: 0.9630 (mmmt) cc_final: 0.9334 (mmmm) REVERT: V 5 ASN cc_start: 0.9316 (t0) cc_final: 0.8759 (t0) REVERT: V 10 GLU cc_start: 0.8667 (pm20) cc_final: 0.8396 (pm20) REVERT: V 20 LYS cc_start: 0.9640 (mmmt) cc_final: 0.9417 (mmmm) REVERT: V 32 LYS cc_start: 0.9524 (mmtt) cc_final: 0.8733 (mtpt) REVERT: W 5 ASN cc_start: 0.9228 (t0) cc_final: 0.8689 (t0) REVERT: W 25 TYR cc_start: 0.9478 (m-80) cc_final: 0.9091 (m-80) REVERT: W 26 LYS cc_start: 0.9163 (ptmm) cc_final: 0.8870 (ptmm) REVERT: X 5 ASN cc_start: 0.9148 (t0) cc_final: 0.8661 (t0) REVERT: X 26 LYS cc_start: 0.9547 (OUTLIER) cc_final: 0.9174 (ptpp) REVERT: X 32 LYS cc_start: 0.9543 (mmtt) cc_final: 0.8709 (ttpt) REVERT: Y 25 TYR cc_start: 0.9566 (m-80) cc_final: 0.9288 (m-80) outliers start: 2 outliers final: 0 residues processed: 143 average time/residue: 0.3674 time to fit residues: 62.1569 Evaluate side-chains 137 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 1 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 7825 Z= 0.307 Angle : 0.607 5.774 10375 Z= 0.308 Chirality : 0.044 0.108 850 Planarity : 0.004 0.027 1350 Dihedral : 3.974 20.159 1075 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 0.52 % Allowed : 11.23 % 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: -0.55 (0.28), residues: 950 helix: 1.68 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.13 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP U 8 HIS 0.002 0.001 HIS Y 18 PHE 0.007 0.001 PHE Y 35 TYR 0.015 0.001 TYR G 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 135 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 0.889 Fit side-chains REVERT: D 20 LYS cc_start: 0.9619 (mmmt) cc_final: 0.9354 (mmmm) REVERT: D 25 TYR cc_start: 0.9559 (m-80) cc_final: 0.9307 (m-80) REVERT: G 11 ASP cc_start: 0.8069 (t0) cc_final: 0.7653 (t0) REVERT: I 5 ASN cc_start: 0.9309 (t0) cc_final: 0.8678 (t0) REVERT: I 11 ASP cc_start: 0.8011 (t0) cc_final: 0.7317 (t0) REVERT: I 13 MET cc_start: 0.8320 (mmm) cc_final: 0.8054 (mpp) REVERT: J 20 LYS cc_start: 0.9660 (mmmt) cc_final: 0.9396 (mmmm) REVERT: J 23 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8910 (mtmm) REVERT: K 5 ASN cc_start: 0.9316 (t0) cc_final: 0.8786 (t0) REVERT: M 5 ASN cc_start: 0.9289 (t0) cc_final: 0.8725 (t0) REVERT: O 5 ASN cc_start: 0.9295 (t0) cc_final: 0.8735 (t0) REVERT: O 10 GLU cc_start: 0.8772 (pm20) cc_final: 0.8434 (pm20) REVERT: P 20 LYS cc_start: 0.9636 (mmmt) cc_final: 0.9244 (mmmm) REVERT: R 5 ASN cc_start: 0.9443 (t0) cc_final: 0.8900 (t0) REVERT: T 5 ASN cc_start: 0.9423 (t0) cc_final: 0.8981 (t0) REVERT: T 20 LYS cc_start: 0.9643 (mmmt) cc_final: 0.9354 (mmmm) REVERT: V 5 ASN cc_start: 0.9436 (t0) cc_final: 0.8925 (t0) REVERT: V 11 ASP cc_start: 0.8135 (t0) cc_final: 0.7928 (t0) REVERT: V 20 LYS cc_start: 0.9657 (mmmt) cc_final: 0.9443 (mmmm) REVERT: V 32 LYS cc_start: 0.9557 (mmtt) cc_final: 0.8770 (mtpt) REVERT: W 5 ASN cc_start: 0.9363 (t0) cc_final: 0.8905 (t0) REVERT: W 25 TYR cc_start: 0.9565 (m-80) cc_final: 0.9353 (m-80) REVERT: W 26 LYS cc_start: 0.9181 (ptmm) cc_final: 0.8853 (ptmm) REVERT: X 5 ASN cc_start: 0.9303 (t0) cc_final: 0.8851 (t0) REVERT: X 26 LYS cc_start: 0.9513 (OUTLIER) cc_final: 0.9169 (ptpp) REVERT: X 32 LYS cc_start: 0.9581 (mmtt) cc_final: 0.8782 (ttpt) REVERT: Y 25 TYR cc_start: 0.9611 (m-80) cc_final: 0.9103 (m-80) outliers start: 4 outliers final: 1 residues processed: 132 average time/residue: 0.3624 time to fit residues: 56.8713 Evaluate side-chains 131 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 MET 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 19 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.0980 chunk 93 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7825 Z= 0.165 Angle : 0.549 6.549 10375 Z= 0.281 Chirality : 0.042 0.110 850 Planarity : 0.003 0.025 1350 Dihedral : 3.690 19.810 1075 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.26 % Allowed : 12.39 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.28), residues: 950 helix: 1.80 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.12 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 8 HIS 0.002 0.000 HIS L 18 PHE 0.005 0.001 PHE Y 35 TYR 0.016 0.001 TYR H 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 148 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 0.904 Fit side-chains REVERT: B 5 ASN cc_start: 0.9239 (t0) cc_final: 0.8837 (t0) REVERT: D 20 LYS cc_start: 0.9632 (mmmt) cc_final: 0.9360 (mmmm) REVERT: E 20 LYS cc_start: 0.9571 (mmmt) cc_final: 0.9366 (mmmm) REVERT: G 5 ASN cc_start: 0.9179 (t0) cc_final: 0.8518 (t0) REVERT: G 11 ASP cc_start: 0.7995 (t0) cc_final: 0.7643 (t0) REVERT: I 5 ASN cc_start: 0.9165 (t0) cc_final: 0.8450 (t0) REVERT: J 20 LYS cc_start: 0.9664 (mmmt) cc_final: 0.9390 (mmmm) REVERT: J 23 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8940 (mtmm) REVERT: K 5 ASN cc_start: 0.9190 (t0) cc_final: 0.8565 (t0) REVERT: K 10 GLU cc_start: 0.8731 (pm20) cc_final: 0.8488 (pm20) REVERT: L 20 LYS cc_start: 0.9659 (mmmt) cc_final: 0.9406 (mmmm) REVERT: M 5 ASN cc_start: 0.9174 (t0) cc_final: 0.8516 (t0) REVERT: O 5 ASN cc_start: 0.9185 (t0) cc_final: 0.8588 (t0) REVERT: P 5 ASN cc_start: 0.9296 (t0) cc_final: 0.8949 (t0) REVERT: P 20 LYS cc_start: 0.9632 (mmmt) cc_final: 0.9268 (mmmm) REVERT: Q 5 ASN cc_start: 0.9162 (t0) cc_final: 0.8621 (t0) REVERT: Q 20 LYS cc_start: 0.9672 (mmmt) cc_final: 0.9463 (mmmm) REVERT: Q 25 TYR cc_start: 0.9552 (m-80) cc_final: 0.9245 (m-80) REVERT: R 5 ASN cc_start: 0.9284 (t0) cc_final: 0.8852 (t0) REVERT: S 20 LYS cc_start: 0.9634 (mmmt) cc_final: 0.9430 (mmmm) REVERT: T 5 ASN cc_start: 0.9303 (t0) cc_final: 0.8755 (t0) REVERT: T 20 LYS cc_start: 0.9638 (mmmt) cc_final: 0.9327 (mmmm) REVERT: U 20 LYS cc_start: 0.9691 (mmmt) cc_final: 0.9481 (mmmm) REVERT: V 5 ASN cc_start: 0.9310 (t0) cc_final: 0.8753 (t0) REVERT: V 10 GLU cc_start: 0.8573 (pm20) cc_final: 0.8291 (pm20) REVERT: V 11 ASP cc_start: 0.8123 (t0) cc_final: 0.7916 (t0) REVERT: V 20 LYS cc_start: 0.9644 (mmmt) cc_final: 0.9419 (mmmm) REVERT: V 32 LYS cc_start: 0.9512 (mmtt) cc_final: 0.8698 (mtpt) REVERT: W 5 ASN cc_start: 0.9230 (t0) cc_final: 0.8695 (t0) REVERT: W 25 TYR cc_start: 0.9554 (m-80) cc_final: 0.9245 (m-80) REVERT: W 26 LYS cc_start: 0.9176 (ptmm) cc_final: 0.8855 (ptmm) REVERT: X 5 ASN cc_start: 0.9149 (t0) cc_final: 0.8658 (t0) REVERT: X 26 LYS cc_start: 0.9497 (OUTLIER) cc_final: 0.9151 (ptpp) REVERT: X 32 LYS cc_start: 0.9528 (mmtt) cc_final: 0.8817 (mtpt) REVERT: Y 25 TYR cc_start: 0.9615 (m-80) cc_final: 0.9154 (m-80) outliers start: 2 outliers final: 0 residues processed: 146 average time/residue: 0.3526 time to fit residues: 61.1548 Evaluate side-chains 141 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 0.0270 chunk 57 optimal weight: 7.9990 overall best weight: 2.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 7825 Z= 0.242 Angle : 0.591 6.956 10375 Z= 0.300 Chirality : 0.043 0.109 850 Planarity : 0.003 0.026 1350 Dihedral : 3.725 20.106 1075 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 0.52 % Allowed : 13.42 % Favored : 86.06 % 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 (0.28), residues: 950 helix: 2.07 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.14 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 8 HIS 0.002 0.001 HIS G 18 PHE 0.005 0.001 PHE Y 35 TYR 0.014 0.001 TYR K 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 145 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 0.940 Fit side-chains REVERT: C 10 GLU cc_start: 0.8738 (pm20) cc_final: 0.8481 (pm20) REVERT: D 20 LYS cc_start: 0.9649 (mmmt) cc_final: 0.9370 (mmmm) REVERT: G 5 ASN cc_start: 0.9239 (t0) cc_final: 0.8605 (t0) REVERT: G 11 ASP cc_start: 0.8022 (t0) cc_final: 0.7649 (t0) REVERT: G 20 LYS cc_start: 0.9592 (mmmt) cc_final: 0.9344 (mmmm) REVERT: G 25 TYR cc_start: 0.9535 (m-80) cc_final: 0.9267 (m-80) REVERT: I 5 ASN cc_start: 0.9233 (t0) cc_final: 0.8548 (t0) REVERT: J 20 LYS cc_start: 0.9676 (mmmt) cc_final: 0.9403 (mmmm) REVERT: J 23 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8939 (mtmm) REVERT: K 5 ASN cc_start: 0.9231 (t0) cc_final: 0.8647 (t0) REVERT: L 20 LYS cc_start: 0.9678 (mmmt) cc_final: 0.9407 (mmmm) REVERT: M 5 ASN cc_start: 0.9213 (t0) cc_final: 0.8567 (t0) REVERT: M 10 GLU cc_start: 0.8821 (pm20) cc_final: 0.8569 (pm20) REVERT: O 5 ASN cc_start: 0.9252 (t0) cc_final: 0.8655 (t0) REVERT: O 10 GLU cc_start: 0.8763 (pm20) cc_final: 0.8457 (pm20) REVERT: P 5 ASN cc_start: 0.9371 (t0) cc_final: 0.8851 (t0) REVERT: P 20 LYS cc_start: 0.9637 (mmmt) cc_final: 0.9275 (mmmm) REVERT: Q 5 ASN cc_start: 0.9232 (t0) cc_final: 0.8688 (t0) REVERT: Q 25 TYR cc_start: 0.9580 (m-80) cc_final: 0.9330 (m-80) REVERT: R 5 ASN cc_start: 0.9364 (t0) cc_final: 0.8929 (t0) REVERT: T 5 ASN cc_start: 0.9364 (t0) cc_final: 0.8827 (t0) REVERT: T 10 GLU cc_start: 0.8651 (pm20) cc_final: 0.8414 (pm20) REVERT: T 20 LYS cc_start: 0.9668 (mmmt) cc_final: 0.9364 (mmmm) REVERT: U 20 LYS cc_start: 0.9701 (mmmt) cc_final: 0.9488 (mmmm) REVERT: V 5 ASN cc_start: 0.9355 (t0) cc_final: 0.8829 (t0) REVERT: V 20 LYS cc_start: 0.9664 (mmmt) cc_final: 0.9437 (mmmm) REVERT: V 32 LYS cc_start: 0.9534 (mmtt) cc_final: 0.8738 (mtpt) REVERT: W 5 ASN cc_start: 0.9299 (t0) cc_final: 0.8764 (t0) REVERT: W 25 TYR cc_start: 0.9579 (m-80) cc_final: 0.9376 (m-80) REVERT: W 26 LYS cc_start: 0.9179 (ptmm) cc_final: 0.8852 (ptmm) REVERT: X 5 ASN cc_start: 0.9201 (t0) cc_final: 0.8725 (t0) REVERT: X 26 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9148 (ptpp) REVERT: X 32 LYS cc_start: 0.9556 (mmtt) cc_final: 0.8740 (ttpt) REVERT: Y 25 TYR cc_start: 0.9618 (m-80) cc_final: 0.9093 (m-80) outliers start: 4 outliers final: 1 residues processed: 142 average time/residue: 0.3519 time to fit residues: 59.6735 Evaluate side-chains 144 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain Q residue 13 MET Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7825 Z= 0.220 Angle : 0.597 7.668 10375 Z= 0.303 Chirality : 0.042 0.110 850 Planarity : 0.003 0.026 1350 Dihedral : 3.744 19.863 1075 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 0.39 % Allowed : 14.19 % Favored : 85.42 % 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: -0.38 (0.28), residues: 950 helix: 2.18 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.15 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Q 8 HIS 0.002 0.001 HIS Q 18 PHE 0.005 0.001 PHE Y 35 TYR 0.016 0.001 TYR H 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 147 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 0.914 Fit side-chains REVERT: B 5 ASN cc_start: 0.9252 (t0) cc_final: 0.8855 (t0) REVERT: C 10 GLU cc_start: 0.8761 (pm20) cc_final: 0.8554 (pm20) REVERT: D 20 LYS cc_start: 0.9645 (mmmt) cc_final: 0.9365 (mmmm) REVERT: E 20 LYS cc_start: 0.9616 (mmmt) cc_final: 0.9403 (mmmm) REVERT: F 20 LYS cc_start: 0.9629 (mmmt) cc_final: 0.9360 (mmmm) REVERT: G 5 ASN cc_start: 0.9221 (t0) cc_final: 0.8574 (t0) REVERT: G 11 ASP cc_start: 0.7984 (t0) cc_final: 0.7629 (t0) REVERT: G 25 TYR cc_start: 0.9544 (m-80) cc_final: 0.9266 (m-80) REVERT: I 5 ASN cc_start: 0.9209 (t0) cc_final: 0.8503 (t0) REVERT: J 20 LYS cc_start: 0.9689 (mmmt) cc_final: 0.9406 (mmmm) REVERT: J 23 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8952 (mtmm) REVERT: K 5 ASN cc_start: 0.9220 (t0) cc_final: 0.8609 (t0) REVERT: K 10 GLU cc_start: 0.8730 (pm20) cc_final: 0.8491 (pm20) REVERT: L 20 LYS cc_start: 0.9681 (mmmt) cc_final: 0.9409 (mmmm) REVERT: M 5 ASN cc_start: 0.9193 (t0) cc_final: 0.8523 (t0) REVERT: M 10 GLU cc_start: 0.8862 (pm20) cc_final: 0.8628 (pm20) REVERT: O 5 ASN cc_start: 0.9228 (t0) cc_final: 0.8631 (t0) REVERT: O 10 GLU cc_start: 0.8777 (pm20) cc_final: 0.8486 (pm20) REVERT: P 5 ASN cc_start: 0.9337 (t0) cc_final: 0.8992 (t0) REVERT: P 20 LYS cc_start: 0.9633 (mmmt) cc_final: 0.9261 (mmmm) REVERT: Q 5 ASN cc_start: 0.9194 (t0) cc_final: 0.8648 (t0) REVERT: Q 10 GLU cc_start: 0.8849 (pm20) cc_final: 0.8595 (pm20) REVERT: Q 20 LYS cc_start: 0.9689 (mmmt) cc_final: 0.9480 (mmmm) REVERT: Q 25 TYR cc_start: 0.9589 (m-80) cc_final: 0.9340 (m-80) REVERT: R 5 ASN cc_start: 0.9321 (t0) cc_final: 0.8879 (t0) REVERT: S 20 LYS cc_start: 0.9662 (mmmt) cc_final: 0.9456 (mmmm) REVERT: T 5 ASN cc_start: 0.9338 (t0) cc_final: 0.8790 (t0) REVERT: T 20 LYS cc_start: 0.9679 (mmmt) cc_final: 0.9378 (mmmm) REVERT: U 20 LYS cc_start: 0.9707 (mmmt) cc_final: 0.9488 (mmmm) REVERT: V 5 ASN cc_start: 0.9327 (t0) cc_final: 0.8772 (t0) REVERT: V 10 GLU cc_start: 0.8565 (pm20) cc_final: 0.8309 (pm20) REVERT: V 20 LYS cc_start: 0.9672 (mmmt) cc_final: 0.9440 (mmmm) REVERT: V 32 LYS cc_start: 0.9523 (mmtt) cc_final: 0.8701 (mtpt) REVERT: W 5 ASN cc_start: 0.9272 (t0) cc_final: 0.8727 (t0) REVERT: W 25 TYR cc_start: 0.9569 (m-80) cc_final: 0.9350 (m-80) REVERT: W 26 LYS cc_start: 0.9181 (ptmm) cc_final: 0.8946 (ptmm) REVERT: X 5 ASN cc_start: 0.9176 (t0) cc_final: 0.8653 (t0) REVERT: X 26 LYS cc_start: 0.9476 (OUTLIER) cc_final: 0.9145 (ptpp) REVERT: X 32 LYS cc_start: 0.9540 (mmtt) cc_final: 0.8858 (mtpt) REVERT: Y 25 TYR cc_start: 0.9611 (m-80) cc_final: 0.9094 (m-80) outliers start: 3 outliers final: 1 residues processed: 144 average time/residue: 0.3640 time to fit residues: 62.3519 Evaluate side-chains 144 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain Q residue 13 MET Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7825 Z= 0.169 Angle : 0.598 8.258 10375 Z= 0.300 Chirality : 0.041 0.113 850 Planarity : 0.003 0.025 1350 Dihedral : 3.488 19.999 1075 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 0.52 % Allowed : 14.32 % Favored : 85.16 % 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: -0.34 (0.28), residues: 950 helix: 2.24 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.13 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 8 HIS 0.002 0.000 HIS G 18 PHE 0.004 0.001 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 157 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 0.846 Fit side-chains REVERT: A 26 LYS cc_start: 0.9531 (ptpp) cc_final: 0.9310 (ptmt) REVERT: B 5 ASN cc_start: 0.9148 (t0) cc_final: 0.8709 (t0) REVERT: D 5 ASN cc_start: 0.9217 (t0) cc_final: 0.8771 (t0) REVERT: D 20 LYS cc_start: 0.9645 (mmmt) cc_final: 0.9373 (mmmm) REVERT: E 20 LYS cc_start: 0.9604 (mmmt) cc_final: 0.9386 (mmmm) REVERT: F 5 ASN cc_start: 0.9233 (t0) cc_final: 0.8801 (t0) REVERT: F 20 LYS cc_start: 0.9626 (mmmt) cc_final: 0.9360 (mmmm) REVERT: G 5 ASN cc_start: 0.9121 (t0) cc_final: 0.8432 (t0) REVERT: G 11 ASP cc_start: 0.7939 (t0) cc_final: 0.7616 (t0) REVERT: G 25 TYR cc_start: 0.9515 (m-80) cc_final: 0.9314 (m-80) REVERT: H 20 LYS cc_start: 0.9621 (mmmt) cc_final: 0.9375 (mmmm) REVERT: I 5 ASN cc_start: 0.9087 (t0) cc_final: 0.8362 (t0) REVERT: J 20 LYS cc_start: 0.9680 (mmmt) cc_final: 0.9399 (mmmm) REVERT: J 23 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8983 (mtmm) REVERT: K 5 ASN cc_start: 0.9111 (t0) cc_final: 0.8474 (t0) REVERT: K 10 GLU cc_start: 0.8761 (pm20) cc_final: 0.8527 (pm20) REVERT: L 20 LYS cc_start: 0.9680 (mmmt) cc_final: 0.9413 (mmmm) REVERT: M 5 ASN cc_start: 0.9071 (t0) cc_final: 0.8494 (t0) REVERT: M 10 GLU cc_start: 0.8839 (pm20) cc_final: 0.8634 (pm20) REVERT: N 5 ASN cc_start: 0.9252 (t0) cc_final: 0.8841 (t0) REVERT: O 5 ASN cc_start: 0.9128 (t0) cc_final: 0.8514 (t0) REVERT: O 10 GLU cc_start: 0.8753 (pm20) cc_final: 0.8469 (pm20) REVERT: P 5 ASN cc_start: 0.9257 (t0) cc_final: 0.8887 (t0) REVERT: P 20 LYS cc_start: 0.9622 (mmmt) cc_final: 0.9244 (mmmm) REVERT: Q 5 ASN cc_start: 0.9083 (t0) cc_final: 0.8613 (t0) REVERT: Q 10 GLU cc_start: 0.8851 (pm20) cc_final: 0.8623 (pm20) REVERT: Q 25 TYR cc_start: 0.9553 (m-80) cc_final: 0.9318 (m-80) REVERT: R 5 ASN cc_start: 0.9225 (t0) cc_final: 0.8799 (t0) REVERT: S 5 ASN cc_start: 0.9037 (t0) cc_final: 0.8565 (t0) REVERT: S 20 LYS cc_start: 0.9650 (mmmt) cc_final: 0.9443 (mmmm) REVERT: T 5 ASN cc_start: 0.9260 (t0) cc_final: 0.8835 (t0) REVERT: T 20 LYS cc_start: 0.9673 (mmmt) cc_final: 0.9366 (mmmm) REVERT: U 20 LYS cc_start: 0.9706 (mmmt) cc_final: 0.9494 (mmmm) REVERT: V 5 ASN cc_start: 0.9234 (t0) cc_final: 0.8672 (t0) REVERT: V 10 GLU cc_start: 0.8615 (pm20) cc_final: 0.8376 (pm20) REVERT: V 20 LYS cc_start: 0.9662 (mmmt) cc_final: 0.9427 (mmmm) REVERT: V 25 TYR cc_start: 0.9430 (m-80) cc_final: 0.8733 (m-80) REVERT: V 32 LYS cc_start: 0.9497 (mmtt) cc_final: 0.8682 (mtpt) REVERT: W 5 ASN cc_start: 0.9170 (t0) cc_final: 0.8634 (t0) REVERT: W 25 TYR cc_start: 0.9561 (m-80) cc_final: 0.9284 (m-80) REVERT: W 26 LYS cc_start: 0.9192 (ptmm) cc_final: 0.8869 (ptmm) REVERT: X 5 ASN cc_start: 0.9081 (t0) cc_final: 0.8592 (t0) REVERT: X 26 LYS cc_start: 0.9460 (OUTLIER) cc_final: 0.9157 (ptpp) REVERT: X 32 LYS cc_start: 0.9505 (mmtt) cc_final: 0.8754 (mtpt) REVERT: Y 25 TYR cc_start: 0.9606 (m-80) cc_final: 0.9124 (m-80) outliers start: 4 outliers final: 1 residues processed: 154 average time/residue: 0.3562 time to fit residues: 65.1658 Evaluate side-chains 150 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain Q residue 13 MET Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7825 Z= 0.223 Angle : 0.641 8.364 10375 Z= 0.321 Chirality : 0.042 0.111 850 Planarity : 0.003 0.025 1350 Dihedral : 3.540 20.195 1075 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 0.39 % Allowed : 14.71 % Favored : 84.90 % 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: -0.32 (0.28), residues: 950 helix: 2.33 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -1.14 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 8 HIS 0.002 0.001 HIS Q 18 PHE 0.005 0.001 PHE Y 35 TYR 0.017 0.001 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 149 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 146 time to evaluate : 0.805 Fit side-chains REVERT: B 5 ASN cc_start: 0.9229 (t0) cc_final: 0.8827 (t0) REVERT: D 5 ASN cc_start: 0.9288 (t0) cc_final: 0.8857 (t0) REVERT: D 20 LYS cc_start: 0.9641 (mmmt) cc_final: 0.9436 (mmmm) REVERT: E 20 LYS cc_start: 0.9630 (mmmt) cc_final: 0.9412 (mmmm) REVERT: F 20 LYS cc_start: 0.9637 (mmmt) cc_final: 0.9366 (mmmm) REVERT: G 5 ASN cc_start: 0.9194 (t0) cc_final: 0.8510 (t0) REVERT: G 11 ASP cc_start: 0.7949 (t0) cc_final: 0.7606 (t0) REVERT: G 25 TYR cc_start: 0.9555 (m-80) cc_final: 0.9302 (m-80) REVERT: H 20 LYS cc_start: 0.9632 (mmmt) cc_final: 0.9386 (mmmm) REVERT: I 5 ASN cc_start: 0.9189 (t0) cc_final: 0.8449 (t0) REVERT: J 20 LYS cc_start: 0.9684 (mmmt) cc_final: 0.9400 (mmmm) REVERT: J 23 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8980 (mtmm) REVERT: K 5 ASN cc_start: 0.9177 (t0) cc_final: 0.8535 (t0) REVERT: K 10 GLU cc_start: 0.8757 (pm20) cc_final: 0.8521 (pm20) REVERT: L 20 LYS cc_start: 0.9691 (mmmt) cc_final: 0.9420 (mmmm) REVERT: M 5 ASN cc_start: 0.9156 (t0) cc_final: 0.8504 (t0) REVERT: M 10 GLU cc_start: 0.8875 (pm20) cc_final: 0.8665 (pm20) REVERT: O 5 ASN cc_start: 0.9188 (t0) cc_final: 0.8566 (t0) REVERT: O 10 GLU cc_start: 0.8783 (pm20) cc_final: 0.8506 (pm20) REVERT: P 5 ASN cc_start: 0.9310 (t0) cc_final: 0.8917 (t0) REVERT: P 20 LYS cc_start: 0.9627 (mmmt) cc_final: 0.9253 (mmmm) REVERT: Q 5 ASN cc_start: 0.9147 (t0) cc_final: 0.8669 (t0) REVERT: Q 10 GLU cc_start: 0.8895 (pm20) cc_final: 0.8677 (pm20) REVERT: R 5 ASN cc_start: 0.9305 (t0) cc_final: 0.8878 (t0) REVERT: S 5 ASN cc_start: 0.9107 (t0) cc_final: 0.8649 (t0) REVERT: S 20 LYS cc_start: 0.9673 (mmmt) cc_final: 0.9463 (mmmm) REVERT: T 5 ASN cc_start: 0.9303 (t0) cc_final: 0.8938 (t0) REVERT: T 20 LYS cc_start: 0.9687 (mmmt) cc_final: 0.9388 (mmmm) REVERT: U 20 LYS cc_start: 0.9702 (mmmt) cc_final: 0.9482 (mmmm) REVERT: V 5 ASN cc_start: 0.9312 (t0) cc_final: 0.8750 (t0) REVERT: V 10 GLU cc_start: 0.8598 (pm20) cc_final: 0.8379 (pm20) REVERT: V 20 LYS cc_start: 0.9664 (mmmt) cc_final: 0.9434 (mmmm) REVERT: V 25 TYR cc_start: 0.9470 (m-80) cc_final: 0.8803 (m-80) REVERT: V 32 LYS cc_start: 0.9517 (mmtt) cc_final: 0.8689 (mtpt) REVERT: W 5 ASN cc_start: 0.9229 (t0) cc_final: 0.8684 (t0) REVERT: W 25 TYR cc_start: 0.9573 (m-80) cc_final: 0.9355 (m-80) REVERT: W 26 LYS cc_start: 0.9192 (ptmm) cc_final: 0.8853 (ptmm) REVERT: X 5 ASN cc_start: 0.9152 (t0) cc_final: 0.8607 (t0) REVERT: X 26 LYS cc_start: 0.9453 (OUTLIER) cc_final: 0.9135 (ptpp) REVERT: X 32 LYS cc_start: 0.9541 (mmtt) cc_final: 0.8704 (ttpt) REVERT: Y 13 MET cc_start: 0.7938 (mmt) cc_final: 0.7613 (mmm) REVERT: Y 25 TYR cc_start: 0.9602 (m-80) cc_final: 0.9120 (m-80) outliers start: 3 outliers final: 1 residues processed: 146 average time/residue: 0.3567 time to fit residues: 61.9336 Evaluate side-chains 148 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 145 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain Q residue 13 MET Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 57 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 = 0.2941 r_free = 0.2941 target = 0.035878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2296 r_free = 0.2296 target = 0.021366 restraints weight = 39494.965| |-----------------------------------------------------------------------------| r_work (start): 0.2249 rms_B_bonded: 5.07 r_work: 0.2107 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.2107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 7825 Z= 0.385 Angle : 0.713 8.693 10375 Z= 0.358 Chirality : 0.045 0.115 850 Planarity : 0.004 0.026 1350 Dihedral : 4.212 22.171 1075 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.39 % Allowed : 15.23 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.29), residues: 950 helix: 2.47 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -1.27 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1964.54 seconds wall clock time: 37 minutes 0.84 seconds (2220.84 seconds total)