Starting phenix.real_space_refine on Tue Sep 24 20:05:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/09_2024/8azs_15770.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/09_2024/8azs_15770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/09_2024/8azs_15770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/09_2024/8azs_15770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/09_2024/8azs_15770.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/09_2024/8azs_15770.cif" } resolution = 2.9 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= 0.002 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 36 5.16 5 C 5868 2.51 5 N 1512 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9036 Number of models: 1 Model: "" Number of chains: 1 Chain: "1" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Restraints were copied for chains: 0, 3, 2, 5, 4, 7, 6, 9, 8, A, C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z Time building chain proxies: 2.46, per 1000 atoms: 0.27 Number of scatterers: 9036 At special positions: 0 Unit cell: (73.959, 63.987, 45.705, 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 36 16.00 O 1620 8.00 N 1512 7.00 C 5868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 15.36 Conformation dependent library (CDL) restraints added in 1.2 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 15.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2250 1.33 - 1.45: 2149 1.45 - 1.57: 4709 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 9180 Sorted by residual: bond pdb=" CE1 HIS G 13 " pdb=" NE2 HIS G 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.92e+01 bond pdb=" CE1 HIS N 13 " pdb=" NE2 HIS N 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.92e+01 bond pdb=" CE1 HIS 6 13 " pdb=" NE2 HIS 6 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.91e+01 bond pdb=" CE1 HIS 0 13 " pdb=" NE2 HIS 0 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.91e+01 bond pdb=" CE1 HIS O 13 " pdb=" NE2 HIS O 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.91e+01 ... (remaining 9175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 8726 1.41 - 2.82: 2830 2.82 - 4.24: 612 4.24 - 5.65: 108 5.65 - 7.06: 72 Bond angle restraints: 12348 Sorted by residual: angle pdb=" C GLN 5 15 " pdb=" CA GLN 5 15 " pdb=" CB GLN 5 15 " ideal model delta sigma weight residual 109.53 115.42 -5.89 1.69e+00 3.50e-01 1.22e+01 angle pdb=" C GLN Z 15 " pdb=" CA GLN Z 15 " pdb=" CB GLN Z 15 " ideal model delta sigma weight residual 109.53 115.42 -5.89 1.69e+00 3.50e-01 1.22e+01 angle pdb=" C GLN K 15 " pdb=" CA GLN K 15 " pdb=" CB GLN K 15 " ideal model delta sigma weight residual 109.53 115.42 -5.89 1.69e+00 3.50e-01 1.22e+01 angle pdb=" C GLN Q 15 " pdb=" CA GLN Q 15 " pdb=" CB GLN Q 15 " ideal model delta sigma weight residual 109.53 115.42 -5.89 1.69e+00 3.50e-01 1.22e+01 angle pdb=" C GLN 9 15 " pdb=" CA GLN 9 15 " pdb=" CB GLN 9 15 " ideal model delta sigma weight residual 109.53 115.40 -5.87 1.69e+00 3.50e-01 1.21e+01 ... (remaining 12343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4644 17.38 - 34.75: 288 34.75 - 52.13: 144 52.13 - 69.51: 0 69.51 - 86.89: 36 Dihedral angle restraints: 5112 sinusoidal: 1872 harmonic: 3240 Sorted by residual: dihedral pdb=" CA VAL T 36 " pdb=" C VAL T 36 " pdb=" N GLY T 37 " pdb=" CA GLY T 37 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA VAL A 36 " pdb=" C VAL A 36 " pdb=" N GLY A 37 " pdb=" CA GLY A 37 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA VAL U 36 " pdb=" C VAL U 36 " pdb=" N GLY U 37 " pdb=" CA GLY U 37 " ideal model delta harmonic sigma weight residual -180.00 -161.81 -18.19 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 247 0.047 - 0.093: 437 0.093 - 0.139: 351 0.139 - 0.186: 297 0.186 - 0.232: 72 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CB ILE W 31 " pdb=" CA ILE W 31 " pdb=" CG1 ILE W 31 " pdb=" CG2 ILE W 31 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE D 31 " pdb=" CA ILE D 31 " pdb=" CG1 ILE D 31 " pdb=" CG2 ILE D 31 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE I 31 " pdb=" CA ILE I 31 " pdb=" CG1 ILE I 31 " pdb=" CG2 ILE I 31 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1401 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS 3 14 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C HIS 3 14 " 0.041 2.00e-02 2.50e+03 pdb=" O HIS 3 14 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN 3 15 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS 9 14 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C HIS 9 14 " 0.041 2.00e-02 2.50e+03 pdb=" O HIS 9 14 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN 9 15 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 14 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C HIS A 14 " -0.041 2.00e-02 2.50e+03 pdb=" O HIS A 14 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 15 " 0.014 2.00e-02 2.50e+03 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 0.02 - 0.99: 5996 0.99 - 1.97: 19210 1.97 - 2.95: 66996 2.95 - 3.92: 129811 3.92 - 4.90: 183018 Warning: very small nonbonded interaction distances. Nonbonded interactions: 405031 Sorted by model distance: nonbonded pdb=" CD1 LEU S 34 " pdb=" CD1 LEU 5 34 " model vdw 0.017 3.880 nonbonded pdb=" CD1 LEU K 34 " pdb=" CD1 LEU H 34 " model vdw 0.017 3.880 nonbonded pdb=" CD1 LEU H 34 " pdb=" CD1 LEU Z 34 " model vdw 0.017 3.880 nonbonded pdb=" CD1 LEU Q 34 " pdb=" CD1 LEU S 34 " model vdw 0.017 3.880 nonbonded pdb=" CD2 LEU L 34 " pdb=" CD2 LEU C 34 " model vdw 0.017 3.880 ... (remaining 405026 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = 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' selection = chain 'Z' } 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: 0.820 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 33.370 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.072 9180 Z= 0.768 Angle : 1.502 7.059 12348 Z= 0.989 Chirality : 0.115 0.232 1404 Planarity : 0.008 0.024 1584 Dihedral : 16.095 86.885 3096 Min Nonbonded Distance : 0.017 Molprobity Statistics. All-atom Clashscore : 1346.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % 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: -1.98 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS P 13 PHE 0.031 0.009 PHE Z 19 TYR 0.017 0.004 TYR Z 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 TYR cc_start: 0.6000 (m-80) cc_final: 0.5728 (m-80) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 1.4457 time to fit residues: 251.7111 Evaluate side-chains 153 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.4980 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 30.0000 chunk 55 optimal weight: 40.0000 chunk 43 optimal weight: 0.0020 chunk 84 optimal weight: 40.0000 chunk 32 optimal weight: 50.0000 chunk 51 optimal weight: 50.0000 chunk 63 optimal weight: 0.0170 chunk 98 optimal weight: 50.0000 overall best weight: 3.1030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1412 moved from start: 7.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.077 0.777 9180 Z= 4.319 Angle : 7.739 64.265 12348 Z= 4.636 Chirality : 0.513 3.986 1404 Planarity : 0.034 0.251 1584 Dihedral : 26.222 92.701 1260 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 874.25 Ramachandran Plot: Outliers : 29.25 % Allowed : 30.56 % Favored : 40.19 % Rotamer: Outliers : 37.67 % Allowed : 18.00 % Favored : 44.33 % Cbeta Deviations : 31.94 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 21.63 % 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: -8.24 (0.12), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.28 (0.09), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.161 0.024 HIS 5 14 PHE 0.199 0.033 PHE 7 19 TYR 0.124 0.022 TYR K 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 128 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 11 GLU cc_start: 0.2383 (OUTLIER) cc_final: 0.2007 (mp0) REVERT: L 15 GLN cc_start: -0.0838 (OUTLIER) cc_final: -0.1643 (mt0) REVERT: M 41 ILE cc_start: -0.0154 (OUTLIER) cc_final: -0.1150 (mt) REVERT: O 15 GLN cc_start: -0.2897 (OUTLIER) cc_final: -0.3247 (mp10) REVERT: O 23 ASP cc_start: 0.2059 (OUTLIER) cc_final: 0.1761 (t0) REVERT: P 35 MET cc_start: 0.1911 (ttt) cc_final: 0.1543 (ttp) REVERT: Q 22 GLU cc_start: 0.2455 (OUTLIER) cc_final: 0.1908 (tt0) REVERT: H 31 ILE cc_start: 0.3048 (OUTLIER) cc_final: 0.2200 (pt) REVERT: A 10 TYR cc_start: 0.2275 (m-80) cc_final: 0.1765 (m-80) REVERT: D 19 PHE cc_start: -0.0293 (OUTLIER) cc_final: -0.0739 (t80) REVERT: Y 14 HIS cc_start: 0.1415 (OUTLIER) cc_final: 0.0330 (m90) REVERT: Y 17 LEU cc_start: 0.3843 (OUTLIER) cc_final: 0.3569 (tt) REVERT: 0 41 ILE cc_start: 0.0425 (OUTLIER) cc_final: -0.1286 (pp) REVERT: 4 32 ILE cc_start: -0.3221 (OUTLIER) cc_final: -0.3852 (pt) REVERT: 6 35 MET cc_start: 0.1503 (OUTLIER) cc_final: 0.1108 (mtt) outliers start: 339 outliers final: 209 residues processed: 417 average time/residue: 0.5883 time to fit residues: 280.8885 Evaluate side-chains 342 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 120 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 22 GLU Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 20 PHE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain M residue 15 GLN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 14 HIS Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain N residue 35 MET Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 27 ASN Chi-restraints excluded: chain P residue 13 HIS Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 27 ASN Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 41 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 20 PHE Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 14 HIS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 14 HIS Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 27 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain T residue 13 HIS Chi-restraints excluded: chain T residue 19 PHE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain V residue 13 HIS Chi-restraints excluded: chain V residue 15 GLN Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 24 VAL Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 19 PHE Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 35 MET Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 14 HIS Chi-restraints excluded: chain X residue 19 PHE Chi-restraints excluded: chain X residue 31 ILE Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 13 HIS Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 20 PHE Chi-restraints excluded: chain Y residue 32 ILE Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 15 GLN Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 19 PHE Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 35 MET Chi-restraints excluded: chain Z residue 41 ILE Chi-restraints excluded: chain 0 residue 11 GLU Chi-restraints excluded: chain 0 residue 13 HIS Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 17 LEU Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 0 residue 34 LEU Chi-restraints excluded: chain 0 residue 35 MET Chi-restraints excluded: chain 0 residue 40 VAL Chi-restraints excluded: chain 0 residue 41 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 15 GLN Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 24 VAL Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 1 residue 34 LEU Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 20 PHE Chi-restraints excluded: chain 2 residue 27 ASN Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 35 MET Chi-restraints excluded: chain 2 residue 40 VAL Chi-restraints excluded: chain 3 residue 16 LYS Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 34 LEU Chi-restraints excluded: chain 3 residue 39 VAL Chi-restraints excluded: chain 4 residue 15 GLN Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 35 MET Chi-restraints excluded: chain 4 residue 40 VAL Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 5 residue 12 VAL Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 19 PHE Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 5 residue 40 VAL Chi-restraints excluded: chain 6 residue 13 HIS Chi-restraints excluded: chain 6 residue 24 VAL Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 6 residue 35 MET Chi-restraints excluded: chain 6 residue 40 VAL Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 24 VAL Chi-restraints excluded: chain 7 residue 34 LEU Chi-restraints excluded: chain 8 residue 10 TYR Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 15 GLN Chi-restraints excluded: chain 8 residue 20 PHE Chi-restraints excluded: chain 9 residue 13 HIS Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 34 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 50.0000 chunk 30 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 HIS ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 HIS ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 13 HIS ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1550 moved from start: 7.9023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.596 9180 Z= 2.649 Angle : 5.877 69.937 12348 Z= 3.466 Chirality : 0.305 4.647 1404 Planarity : 0.028 0.103 1584 Dihedral : 25.754 89.615 1260 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 660.87 Ramachandran Plot: Outliers : 20.57 % Allowed : 42.80 % Favored : 36.63 % Rotamer: Outliers : 37.11 % Allowed : 20.56 % Favored : 42.33 % Cbeta Deviations : 15.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 22.98 % 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: -8.48 (0.12), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.46 (0.09), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.058 0.011 HIS 7 14 PHE 0.187 0.026 PHE 6 19 TYR 0.129 0.016 TYR K 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 106 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 19 PHE cc_start: 0.2307 (OUTLIER) cc_final: 0.2082 (m-80) REVERT: I 13 HIS cc_start: 0.3697 (OUTLIER) cc_final: 0.3074 (p90) REVERT: I 17 LEU cc_start: -0.0557 (OUTLIER) cc_final: -0.1032 (mt) REVERT: J 16 LYS cc_start: 0.3995 (tttt) cc_final: 0.3602 (ttpt) REVERT: K 35 MET cc_start: 0.1586 (OUTLIER) cc_final: 0.0845 (ttp) REVERT: N 18 VAL cc_start: 0.3042 (t) cc_final: 0.2834 (t) REVERT: Q 20 PHE cc_start: 0.2054 (OUTLIER) cc_final: 0.1206 (p90) REVERT: R 11 GLU cc_start: 0.0119 (OUTLIER) cc_final: -0.1530 (tm-30) REVERT: A 10 TYR cc_start: 0.3434 (m-80) cc_final: 0.2978 (m-10) REVERT: E 32 ILE cc_start: -0.2874 (OUTLIER) cc_final: -0.3289 (mt) REVERT: Z 41 ILE cc_start: 0.0881 (mm) cc_final: -0.0643 (mt) REVERT: 1 27 ASN cc_start: -0.1620 (OUTLIER) cc_final: -0.3454 (t0) REVERT: 4 12 VAL cc_start: -0.0408 (OUTLIER) cc_final: -0.0645 (t) REVERT: 4 15 GLN cc_start: 0.2228 (OUTLIER) cc_final: 0.1971 (tp40) REVERT: 6 32 ILE cc_start: 0.0945 (OUTLIER) cc_final: 0.0499 (mt) outliers start: 334 outliers final: 205 residues processed: 401 average time/residue: 0.5505 time to fit residues: 253.5998 Evaluate side-chains 314 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 98 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 19 PHE Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain K residue 10 TYR Chi-restraints excluded: chain K residue 20 PHE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 35 MET Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain Q residue 10 TYR Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 20 PHE Chi-restraints excluded: chain Q residue 27 ASN Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 41 ILE Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 27 ASN Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 27 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain T residue 13 HIS Chi-restraints excluded: chain T residue 27 ASN Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 13 HIS Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 35 MET Chi-restraints excluded: chain U residue 40 VAL Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain V residue 10 TYR Chi-restraints excluded: chain V residue 15 GLN Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 14 HIS Chi-restraints excluded: chain W residue 27 ASN Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 19 PHE Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 31 ILE Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain Y residue 13 HIS Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 20 PHE Chi-restraints excluded: chain Y residue 32 ILE Chi-restraints excluded: chain Y residue 35 MET Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 14 HIS Chi-restraints excluded: chain Z residue 15 GLN Chi-restraints excluded: chain Z residue 19 PHE Chi-restraints excluded: chain Z residue 20 PHE Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 27 ASN Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain 0 residue 13 HIS Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 16 LYS Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 0 residue 40 VAL Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 24 VAL Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 1 residue 34 LEU Chi-restraints excluded: chain 2 residue 11 GLU Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 19 PHE Chi-restraints excluded: chain 2 residue 20 PHE Chi-restraints excluded: chain 2 residue 26 SER Chi-restraints excluded: chain 2 residue 31 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 35 MET Chi-restraints excluded: chain 2 residue 41 ILE Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 34 LEU Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 15 GLN Chi-restraints excluded: chain 4 residue 20 PHE Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 14 HIS Chi-restraints excluded: chain 5 residue 19 PHE Chi-restraints excluded: chain 5 residue 20 PHE Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 36 VAL Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 5 residue 40 VAL Chi-restraints excluded: chain 6 residue 13 HIS Chi-restraints excluded: chain 6 residue 24 VAL Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 6 residue 40 VAL Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 24 VAL Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 17 LEU Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 9 residue 15 GLN Chi-restraints excluded: chain 9 residue 20 PHE Chi-restraints excluded: chain 9 residue 22 GLU Chi-restraints excluded: chain 9 residue 23 ASP Chi-restraints excluded: chain 9 residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 15 GLN ** 5 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1453 moved from start: 8.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.041 0.455 9180 Z= 2.121 Angle : 5.046 49.421 12348 Z= 2.921 Chirality : 0.237 1.423 1404 Planarity : 0.024 0.092 1584 Dihedral : 24.772 87.900 1260 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 541.64 Ramachandran Plot: Outliers : 15.02 % Allowed : 48.00 % Favored : 36.98 % Rotamer: Outliers : 35.33 % Allowed : 22.78 % Favored : 41.89 % Cbeta Deviations : 10.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 20.96 % 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: -8.54 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.50 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.045 0.010 HIS 7 14 PHE 0.198 0.024 PHE 7 19 TYR 0.103 0.012 TYR W 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 108 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 LEU cc_start: 0.3432 (OUTLIER) cc_final: 0.3185 (tt) REVERT: I 13 HIS cc_start: 0.3833 (OUTLIER) cc_final: 0.3570 (p90) REVERT: J 27 ASN cc_start: 0.3831 (OUTLIER) cc_final: 0.3372 (t0) REVERT: L 11 GLU cc_start: 0.0131 (OUTLIER) cc_final: -0.0250 (tt0) REVERT: M 16 LYS cc_start: 0.1399 (OUTLIER) cc_final: 0.1154 (ttpt) REVERT: M 17 LEU cc_start: 0.1000 (OUTLIER) cc_final: 0.0782 (tt) REVERT: O 27 ASN cc_start: 0.0534 (OUTLIER) cc_final: -0.1144 (t0) REVERT: R 11 GLU cc_start: -0.0317 (OUTLIER) cc_final: -0.0852 (pt0) REVERT: R 20 PHE cc_start: 0.0482 (OUTLIER) cc_final: 0.0212 (m-10) REVERT: A 10 TYR cc_start: 0.3162 (m-80) cc_final: 0.2557 (m-80) REVERT: A 28 LYS cc_start: -0.1362 (OUTLIER) cc_final: -0.1643 (pttp) REVERT: E 22 GLU cc_start: 0.0898 (OUTLIER) cc_final: 0.0104 (mt-10) REVERT: E 32 ILE cc_start: -0.1977 (OUTLIER) cc_final: -0.2385 (mt) REVERT: S 10 TYR cc_start: -0.0582 (OUTLIER) cc_final: -0.0891 (m-80) REVERT: T 15 GLN cc_start: 0.1070 (OUTLIER) cc_final: 0.0401 (mm-40) REVERT: Z 41 ILE cc_start: 0.1312 (mm) cc_final: 0.0775 (mm) REVERT: 0 20 PHE cc_start: -0.1440 (OUTLIER) cc_final: -0.2302 (m-80) REVERT: 1 23 ASP cc_start: 0.3798 (m-30) cc_final: 0.3535 (p0) REVERT: 2 18 VAL cc_start: 0.5748 (t) cc_final: 0.5546 (p) REVERT: 3 15 GLN cc_start: 0.0337 (OUTLIER) cc_final: -0.0703 (mm-40) REVERT: 4 39 VAL cc_start: 0.2883 (t) cc_final: 0.2137 (t) REVERT: 6 15 GLN cc_start: -0.0099 (OUTLIER) cc_final: -0.0757 (tp40) outliers start: 318 outliers final: 175 residues processed: 383 average time/residue: 0.5562 time to fit residues: 244.9877 Evaluate side-chains 291 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 99 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 11 GLU Chi-restraints excluded: chain L residue 19 PHE Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 35 MET Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain O residue 14 HIS Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 ASN Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain Q residue 10 TYR Chi-restraints excluded: chain Q residue 27 ASN Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 41 ILE Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 20 PHE Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 27 ASN Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain S residue 10 TYR Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 27 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain T residue 13 HIS Chi-restraints excluded: chain T residue 15 GLN Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 27 ASN Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 40 VAL Chi-restraints excluded: chain V residue 10 TYR Chi-restraints excluded: chain V residue 15 GLN Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 14 HIS Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 23 ASP Chi-restraints excluded: chain W residue 27 ASN Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 22 GLU Chi-restraints excluded: chain X residue 31 ILE Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 27 ASN Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 20 PHE Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 27 ASN Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 0 residue 40 VAL Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 15 GLN Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 20 PHE Chi-restraints excluded: chain 2 residue 31 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 35 MET Chi-restraints excluded: chain 2 residue 41 ILE Chi-restraints excluded: chain 3 residue 10 TYR Chi-restraints excluded: chain 3 residue 15 GLN Chi-restraints excluded: chain 3 residue 20 PHE Chi-restraints excluded: chain 3 residue 34 LEU Chi-restraints excluded: chain 4 residue 14 HIS Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 40 VAL Chi-restraints excluded: chain 5 residue 12 VAL Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 14 HIS Chi-restraints excluded: chain 5 residue 20 PHE Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 5 residue 40 VAL Chi-restraints excluded: chain 6 residue 15 GLN Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 6 residue 24 VAL Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 6 residue 36 VAL Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 20 PHE Chi-restraints excluded: chain 7 residue 24 VAL Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 16 LYS Chi-restraints excluded: chain 8 residue 19 PHE Chi-restraints excluded: chain 8 residue 20 PHE Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 9 residue 24 VAL Chi-restraints excluded: chain 9 residue 27 ASN Chi-restraints excluded: chain 9 residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 15 GLN ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1239 moved from start: 8.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.035 0.373 9180 Z= 1.796 Angle : 4.615 54.157 12348 Z= 2.598 Chirality : 0.211 1.474 1404 Planarity : 0.021 0.086 1584 Dihedral : 24.182 84.832 1260 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 464.21 Ramachandran Plot: Outliers : 12.59 % Allowed : 47.14 % Favored : 40.28 % Rotamer: Outliers : 29.11 % Allowed : 26.22 % Favored : 44.67 % Cbeta Deviations : 5.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 20.54 % 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: -8.38 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.38 (0.09), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.033 0.007 HIS O 13 PHE 0.174 0.022 PHE S 19 TYR 0.088 0.009 TYR W 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 104 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 22 GLU cc_start: 0.6143 (mp0) cc_final: 0.5627 (mt-10) REVERT: P 15 GLN cc_start: 0.0460 (OUTLIER) cc_final: -0.2437 (mm-40) REVERT: P 19 PHE cc_start: -0.1937 (OUTLIER) cc_final: -0.2638 (m-80) REVERT: A 10 TYR cc_start: 0.2637 (m-80) cc_final: 0.2356 (m-80) REVERT: B 14 HIS cc_start: 0.2344 (t-170) cc_final: 0.2077 (t-170) REVERT: C 35 MET cc_start: -0.0135 (ttt) cc_final: -0.1643 (ttt) REVERT: D 23 ASP cc_start: 0.3132 (OUTLIER) cc_final: 0.2916 (m-30) REVERT: E 32 ILE cc_start: -0.0443 (OUTLIER) cc_final: -0.0727 (mt) REVERT: V 28 LYS cc_start: 0.1808 (mttp) cc_final: 0.1513 (ptpt) REVERT: Y 10 TYR cc_start: 0.4493 (OUTLIER) cc_final: 0.2579 (m-80) REVERT: Y 15 GLN cc_start: 0.4221 (OUTLIER) cc_final: 0.3937 (tp-100) REVERT: Z 34 LEU cc_start: -0.0369 (OUTLIER) cc_final: -0.1496 (tp) REVERT: Z 41 ILE cc_start: 0.0682 (mm) cc_final: 0.0099 (mp) REVERT: 2 22 GLU cc_start: 0.4174 (mt-10) cc_final: 0.3748 (mt-10) REVERT: 3 36 VAL cc_start: -0.0046 (OUTLIER) cc_final: -0.0341 (t) REVERT: 4 40 VAL cc_start: 0.5012 (OUTLIER) cc_final: 0.4784 (t) REVERT: 5 27 ASN cc_start: -0.1111 (OUTLIER) cc_final: -0.1368 (m-40) REVERT: 5 39 VAL cc_start: 0.2057 (OUTLIER) cc_final: 0.1853 (t) REVERT: 7 28 LYS cc_start: -0.1275 (OUTLIER) cc_final: -0.1863 (ttpt) REVERT: 8 15 GLN cc_start: 0.2680 (OUTLIER) cc_final: 0.2208 (mp10) outliers start: 262 outliers final: 153 residues processed: 339 average time/residue: 0.5948 time to fit residues: 230.1339 Evaluate side-chains 265 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 99 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 20 PHE Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 35 MET Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain S residue 10 TYR Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 27 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 40 VAL Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 14 HIS Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 23 ASP Chi-restraints excluded: chain W residue 27 ASN Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 35 MET Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 19 PHE Chi-restraints excluded: chain X residue 31 ILE Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 10 TYR Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 MET Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 27 ASN Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 0 residue 40 VAL Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 15 GLN Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 31 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 35 MET Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 23 ASP Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 34 LEU Chi-restraints excluded: chain 3 residue 36 VAL Chi-restraints excluded: chain 4 residue 14 HIS Chi-restraints excluded: chain 4 residue 15 GLN Chi-restraints excluded: chain 4 residue 20 PHE Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 40 VAL Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 14 HIS Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 5 residue 40 VAL Chi-restraints excluded: chain 6 residue 10 TYR Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 28 LYS Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 15 GLN Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 32 ILE Chi-restraints excluded: chain 8 residue 34 LEU Chi-restraints excluded: chain 9 residue 23 ASP Chi-restraints excluded: chain 9 residue 24 VAL Chi-restraints excluded: chain 9 residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 HIS ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 HIS ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1419 moved from start: 8.6721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 0.353 9180 Z= 1.639 Angle : 4.298 58.745 12348 Z= 2.391 Chirality : 0.195 1.232 1404 Planarity : 0.019 0.082 1584 Dihedral : 23.944 88.038 1260 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 422.08 Ramachandran Plot: Outliers : 10.33 % Allowed : 49.31 % Favored : 40.36 % Rotamer: Outliers : 29.11 % Allowed : 27.33 % Favored : 43.56 % Cbeta Deviations : 3.87 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 18.94 % 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: -8.35 (0.12), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.36 (0.09), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.028 0.007 HIS 4 14 PHE 0.154 0.020 PHE 7 19 TYR 0.080 0.008 TYR L 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 109 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 ASN cc_start: 0.0328 (OUTLIER) cc_final: -0.0200 (p0) REVERT: G 39 VAL cc_start: -0.1147 (OUTLIER) cc_final: -0.1398 (p) REVERT: J 20 PHE cc_start: 0.7039 (t80) cc_final: 0.6816 (t80) REVERT: P 17 LEU cc_start: -0.3455 (OUTLIER) cc_final: -0.3891 (mp) REVERT: D 34 LEU cc_start: 0.1187 (OUTLIER) cc_final: 0.0756 (tm) REVERT: E 32 ILE cc_start: 0.0014 (OUTLIER) cc_final: -0.0735 (mt) REVERT: X 22 GLU cc_start: 0.2790 (OUTLIER) cc_final: 0.2446 (mm-30) REVERT: Y 28 LYS cc_start: -0.2802 (OUTLIER) cc_final: -0.3142 (ttmt) REVERT: Z 34 LEU cc_start: 0.2166 (OUTLIER) cc_final: 0.1566 (tp) REVERT: 5 35 MET cc_start: -0.0070 (OUTLIER) cc_final: -0.0542 (tpt) REVERT: 7 28 LYS cc_start: -0.0923 (OUTLIER) cc_final: -0.1379 (ttpt) REVERT: 9 15 GLN cc_start: -0.0218 (OUTLIER) cc_final: -0.1207 (mp10) outliers start: 262 outliers final: 153 residues processed: 339 average time/residue: 0.5918 time to fit residues: 229.2424 Evaluate side-chains 265 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 101 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 35 MET Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 20 PHE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain S residue 27 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 15 GLN Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 35 MET Chi-restraints excluded: chain U residue 40 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain W residue 14 HIS Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 23 ASP Chi-restraints excluded: chain W residue 27 ASN Chi-restraints excluded: chain W residue 35 MET Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 22 GLU Chi-restraints excluded: chain X residue 31 ILE Chi-restraints excluded: chain X residue 35 MET Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 28 LYS Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 MET Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 27 ASN Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 0 residue 40 VAL Chi-restraints excluded: chain 1 residue 15 GLN Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 20 PHE Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 15 GLN Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 31 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 35 MET Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 13 HIS Chi-restraints excluded: chain 3 residue 34 LEU Chi-restraints excluded: chain 4 residue 15 GLN Chi-restraints excluded: chain 4 residue 20 PHE Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 14 HIS Chi-restraints excluded: chain 5 residue 16 LYS Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 5 residue 40 VAL Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 20 PHE Chi-restraints excluded: chain 7 residue 28 LYS Chi-restraints excluded: chain 7 residue 40 VAL Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 16 LYS Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 32 ILE Chi-restraints excluded: chain 9 residue 15 GLN Chi-restraints excluded: chain 9 residue 17 LEU Chi-restraints excluded: chain 9 residue 23 ASP Chi-restraints excluded: chain 9 residue 24 VAL Chi-restraints excluded: chain 9 residue 31 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 5.9990 chunk 11 optimal weight: 30.0000 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 HIS ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1500 moved from start: 8.8072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 0.320 9180 Z= 1.531 Angle : 4.129 47.834 12348 Z= 2.277 Chirality : 0.183 0.980 1404 Planarity : 0.018 0.076 1584 Dihedral : 23.805 85.294 1260 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 394.74 Ramachandran Plot: Outliers : 8.68 % Allowed : 49.05 % Favored : 42.27 % Rotamer: Outliers : 24.67 % Allowed : 29.11 % Favored : 46.22 % Cbeta Deviations : 3.97 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 19.44 % 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: -8.25 (0.12), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.28 (0.09), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.040 0.007 HIS V 14 PHE 0.141 0.019 PHE S 19 TYR 0.083 0.007 TYR L 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 116 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 20 PHE cc_start: 0.3107 (OUTLIER) cc_final: 0.1667 (t80) REVERT: G 39 VAL cc_start: -0.0929 (OUTLIER) cc_final: -0.1265 (p) REVERT: G 41 ILE cc_start: 0.3621 (OUTLIER) cc_final: 0.3307 (tt) REVERT: I 15 GLN cc_start: -0.0110 (OUTLIER) cc_final: -0.1382 (tp40) REVERT: J 10 TYR cc_start: -0.1304 (OUTLIER) cc_final: -0.1842 (m-80) REVERT: J 20 PHE cc_start: 0.7174 (t80) cc_final: 0.6708 (t80) REVERT: P 15 GLN cc_start: 0.0982 (OUTLIER) cc_final: -0.1662 (tt0) REVERT: H 17 LEU cc_start: 0.3305 (mp) cc_final: 0.2347 (mp) REVERT: B 14 HIS cc_start: 0.2874 (t70) cc_final: 0.2595 (t70) REVERT: D 15 GLN cc_start: 0.2798 (OUTLIER) cc_final: -0.0675 (tp40) REVERT: E 32 ILE cc_start: 0.0442 (OUTLIER) cc_final: 0.0077 (mt) REVERT: E 40 VAL cc_start: -0.1468 (OUTLIER) cc_final: -0.1786 (p) REVERT: V 22 GLU cc_start: 0.3766 (mp0) cc_final: 0.3412 (mt-10) REVERT: W 14 HIS cc_start: 0.3279 (OUTLIER) cc_final: 0.3066 (t70) REVERT: Y 28 LYS cc_start: -0.2485 (OUTLIER) cc_final: -0.2685 (ttmt) REVERT: Z 34 LEU cc_start: 0.2559 (OUTLIER) cc_final: 0.1710 (tp) REVERT: 2 16 LYS cc_start: 0.1998 (OUTLIER) cc_final: 0.1642 (mttm) REVERT: 3 13 HIS cc_start: 0.2118 (OUTLIER) cc_final: 0.1522 (p-80) REVERT: 8 15 GLN cc_start: 0.3318 (OUTLIER) cc_final: 0.2894 (mt0) outliers start: 222 outliers final: 130 residues processed: 306 average time/residue: 0.6368 time to fit residues: 220.9733 Evaluate side-chains 252 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 107 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 20 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 40 VAL Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 14 HIS Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 23 ASP Chi-restraints excluded: chain W residue 27 ASN Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 35 MET Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 22 GLU Chi-restraints excluded: chain X residue 31 ILE Chi-restraints excluded: chain X residue 35 MET Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain Y residue 16 LYS Chi-restraints excluded: chain Y residue 20 PHE Chi-restraints excluded: chain Y residue 28 LYS Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 MET Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 27 ASN Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 2 residue 15 GLN Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 31 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 35 MET Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 13 HIS Chi-restraints excluded: chain 3 residue 23 ASP Chi-restraints excluded: chain 3 residue 34 LEU Chi-restraints excluded: chain 4 residue 15 GLN Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 40 VAL Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 14 HIS Chi-restraints excluded: chain 5 residue 16 LYS Chi-restraints excluded: chain 5 residue 40 VAL Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 6 residue 40 VAL Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 15 GLN Chi-restraints excluded: chain 8 residue 16 LYS Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain 8 residue 23 ASP Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 9 residue 17 LEU Chi-restraints excluded: chain 9 residue 23 ASP Chi-restraints excluded: chain 9 residue 31 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1511 moved from start: 8.9411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.030 0.273 9180 Z= 1.453 Angle : 4.004 54.508 12348 Z= 2.185 Chirality : 0.177 0.922 1404 Planarity : 0.017 0.078 1584 Dihedral : 23.672 88.212 1260 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 366.96 Ramachandran Plot: Outliers : 8.16 % Allowed : 47.31 % Favored : 44.53 % Rotamer: Outliers : 22.33 % Allowed : 29.78 % Favored : 47.89 % Cbeta Deviations : 3.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 19.44 % 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: -8.15 (0.12), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.21 (0.09), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.039 0.006 HIS Z 13 PHE 0.150 0.018 PHE H 19 TYR 0.074 0.006 TYR L 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 108 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 39 VAL cc_start: -0.0365 (OUTLIER) cc_final: -0.0567 (p) REVERT: O 13 HIS cc_start: 0.2071 (OUTLIER) cc_final: 0.1865 (p90) REVERT: P 41 ILE cc_start: -0.2944 (OUTLIER) cc_final: -0.3343 (OUTLIER) REVERT: R 13 HIS cc_start: 0.2308 (OUTLIER) cc_final: 0.1322 (p90) REVERT: D 15 GLN cc_start: 0.2735 (OUTLIER) cc_final: -0.0521 (mm-40) REVERT: V 22 GLU cc_start: 0.3922 (mt-10) cc_final: 0.3328 (mt-10) REVERT: W 14 HIS cc_start: 0.3827 (OUTLIER) cc_final: 0.3545 (t-90) REVERT: 3 28 LYS cc_start: -0.4976 (OUTLIER) cc_final: -0.5518 (mptt) REVERT: 7 19 PHE cc_start: -0.1577 (OUTLIER) cc_final: -0.2155 (m-80) outliers start: 201 outliers final: 115 residues processed: 281 average time/residue: 0.6785 time to fit residues: 214.4568 Evaluate side-chains 220 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 98 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain T residue 22 GLU Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 14 HIS Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 23 ASP Chi-restraints excluded: chain W residue 27 ASN Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 22 GLU Chi-restraints excluded: chain X residue 35 MET Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 1 residue 10 TYR Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 2 residue 15 GLN Chi-restraints excluded: chain 2 residue 31 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 35 MET Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 23 ASP Chi-restraints excluded: chain 3 residue 28 LYS Chi-restraints excluded: chain 3 residue 34 LEU Chi-restraints excluded: chain 4 residue 15 GLN Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 14 HIS Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 15 GLN Chi-restraints excluded: chain 8 residue 16 LYS Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain 8 residue 20 PHE Chi-restraints excluded: chain 8 residue 23 ASP Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 40 VAL Chi-restraints excluded: chain 9 residue 12 VAL Chi-restraints excluded: chain 9 residue 23 ASP Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 40 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 HIS ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1461 moved from start: 9.0039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.028 0.252 9180 Z= 1.399 Angle : 3.965 54.748 12348 Z= 2.136 Chirality : 0.177 1.588 1404 Planarity : 0.017 0.080 1584 Dihedral : 23.316 84.755 1260 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 354.71 Ramachandran Plot: Outliers : 6.94 % Allowed : 48.78 % Favored : 44.27 % Rotamer: Outliers : 17.56 % Allowed : 33.67 % Favored : 48.78 % Cbeta Deviations : 3.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 19.36 % 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: -8.11 (0.12), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.17 (0.09), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.052 0.006 HIS Z 13 PHE 0.153 0.017 PHE H 19 TYR 0.069 0.006 TYR L 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 107 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 26 SER cc_start: 0.5719 (m) cc_final: 0.5470 (t) REVERT: L 10 TYR cc_start: 0.0574 (OUTLIER) cc_final: -0.0938 (t80) REVERT: P 41 ILE cc_start: -0.2970 (OUTLIER) cc_final: -0.3460 (OUTLIER) REVERT: R 13 HIS cc_start: 0.2267 (OUTLIER) cc_final: 0.1598 (p90) REVERT: H 20 PHE cc_start: 0.0152 (OUTLIER) cc_final: -0.0111 (t80) REVERT: H 34 LEU cc_start: 0.0224 (OUTLIER) cc_final: -0.0293 (tp) REVERT: A 13 HIS cc_start: 0.2248 (OUTLIER) cc_final: 0.1763 (p-80) REVERT: D 15 GLN cc_start: 0.2481 (OUTLIER) cc_final: -0.0309 (mm-40) REVERT: 1 19 PHE cc_start: -0.1259 (OUTLIER) cc_final: -0.4175 (m-80) REVERT: 1 22 GLU cc_start: 0.1485 (mm-30) cc_final: 0.0557 (tt0) REVERT: 2 10 TYR cc_start: 0.3128 (m-80) cc_final: 0.1965 (m-80) REVERT: 3 13 HIS cc_start: 0.2321 (OUTLIER) cc_final: 0.1817 (p-80) REVERT: 3 28 LYS cc_start: -0.5488 (OUTLIER) cc_final: -0.5692 (mmtp) REVERT: 5 17 LEU cc_start: -0.2041 (OUTLIER) cc_final: -0.2750 (tp) REVERT: 8 18 VAL cc_start: 0.1452 (OUTLIER) cc_final: 0.1070 (t) REVERT: 8 23 ASP cc_start: -0.0419 (OUTLIER) cc_final: -0.0815 (m-30) REVERT: 9 40 VAL cc_start: 0.5012 (OUTLIER) cc_final: 0.4547 (m) outliers start: 158 outliers final: 107 residues processed: 239 average time/residue: 0.6788 time to fit residues: 182.3845 Evaluate side-chains 219 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 99 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain K residue 10 TYR Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 41 ILE Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 14 HIS Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 23 ASP Chi-restraints excluded: chain W residue 27 ASN Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 20 PHE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 MET Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 0 residue 35 MET Chi-restraints excluded: chain 1 residue 10 TYR Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 2 residue 15 GLN Chi-restraints excluded: chain 2 residue 31 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 35 MET Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 13 HIS Chi-restraints excluded: chain 3 residue 23 ASP Chi-restraints excluded: chain 3 residue 28 LYS Chi-restraints excluded: chain 3 residue 34 LEU Chi-restraints excluded: chain 4 residue 15 GLN Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 14 HIS Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 6 residue 10 TYR Chi-restraints excluded: chain 6 residue 35 MET Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 8 residue 10 TYR Chi-restraints excluded: chain 8 residue 11 GLU Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 15 GLN Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain 8 residue 20 PHE Chi-restraints excluded: chain 8 residue 23 ASP Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 9 residue 12 VAL Chi-restraints excluded: chain 9 residue 15 GLN Chi-restraints excluded: chain 9 residue 17 LEU Chi-restraints excluded: chain 9 residue 23 ASP Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 HIS ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1444 moved from start: 9.0419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.027 0.252 9180 Z= 1.363 Angle : 3.954 54.768 12348 Z= 2.118 Chirality : 0.170 1.598 1404 Planarity : 0.017 0.100 1584 Dihedral : 23.345 84.218 1260 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 349.24 Ramachandran Plot: Outliers : 6.60 % Allowed : 48.70 % Favored : 44.70 % Rotamer: Outliers : 14.67 % Allowed : 36.67 % Favored : 48.67 % Cbeta Deviations : 3.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 18.77 % 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: -8.10 (0.12), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.17 (0.09), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.046 0.006 HIS Z 13 PHE 0.201 0.016 PHE 7 19 TYR 0.067 0.006 TYR L 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 96 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 26 SER cc_start: 0.5677 (m) cc_final: 0.5428 (t) REVERT: L 10 TYR cc_start: 0.0582 (OUTLIER) cc_final: -0.0991 (t80) REVERT: N 13 HIS cc_start: 0.5186 (OUTLIER) cc_final: 0.2330 (m90) REVERT: Q 16 LYS cc_start: 0.1624 (OUTLIER) cc_final: 0.0693 (mtmt) REVERT: R 13 HIS cc_start: 0.2439 (OUTLIER) cc_final: 0.1992 (p90) REVERT: R 17 LEU cc_start: -0.0243 (OUTLIER) cc_final: -0.0498 (mt) REVERT: H 20 PHE cc_start: -0.0118 (OUTLIER) cc_final: -0.0451 (t80) REVERT: A 15 GLN cc_start: 0.4702 (tp-100) cc_final: 0.4049 (OUTLIER) REVERT: D 15 GLN cc_start: 0.2518 (OUTLIER) cc_final: -0.0131 (mm-40) REVERT: D 32 ILE cc_start: 0.1767 (OUTLIER) cc_final: 0.1534 (mp) REVERT: T 14 HIS cc_start: 0.1667 (t70) cc_final: 0.1332 (t70) REVERT: U 19 PHE cc_start: -0.0456 (OUTLIER) cc_final: -0.2146 (m-80) REVERT: 1 19 PHE cc_start: -0.1038 (OUTLIER) cc_final: -0.2786 (m-80) REVERT: 2 10 TYR cc_start: 0.2704 (m-80) cc_final: 0.1677 (m-80) REVERT: 3 13 HIS cc_start: 0.2170 (OUTLIER) cc_final: 0.1662 (p-80) REVERT: 5 17 LEU cc_start: -0.1968 (OUTLIER) cc_final: -0.2560 (tp) REVERT: 8 23 ASP cc_start: -0.0582 (OUTLIER) cc_final: -0.1018 (m-30) REVERT: 8 35 MET cc_start: 0.2326 (ttt) cc_final: 0.1871 (ttt) REVERT: 9 40 VAL cc_start: 0.4643 (OUTLIER) cc_final: 0.4331 (m) outliers start: 132 outliers final: 94 residues processed: 205 average time/residue: 0.6291 time to fit residues: 146.5610 Evaluate side-chains 202 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 95 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain K residue 10 TYR Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain Q residue 10 TYR Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 23 ASP Chi-restraints excluded: chain W residue 27 ASN Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain Y residue 20 PHE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 MET Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 1 residue 10 TYR Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 2 residue 15 GLN Chi-restraints excluded: chain 2 residue 31 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 3 residue 13 HIS Chi-restraints excluded: chain 3 residue 23 ASP Chi-restraints excluded: chain 3 residue 34 LEU Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 6 residue 10 TYR Chi-restraints excluded: chain 6 residue 35 MET Chi-restraints excluded: chain 8 residue 11 GLU Chi-restraints excluded: chain 8 residue 15 GLN Chi-restraints excluded: chain 8 residue 20 PHE Chi-restraints excluded: chain 8 residue 23 ASP Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 9 residue 12 VAL Chi-restraints excluded: chain 9 residue 17 LEU Chi-restraints excluded: chain 9 residue 23 ASP Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6712 r_free = 0.6712 target = 0.546231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.6697 r_free = 0.6697 target = 0.511662 restraints weight = 10008.400| |-----------------------------------------------------------------------------| r_work (start): 0.6657 rms_B_bonded: 2.38 r_work: 0.6768 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.6675 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.6675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1586 moved from start: 9.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.028 0.293 9180 Z= 1.361 Angle : 3.993 56.084 12348 Z= 2.121 Chirality : 0.174 1.783 1404 Planarity : 0.017 0.098 1584 Dihedral : 23.506 82.192 1260 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 345.81 Ramachandran Plot: Outliers : 7.03 % Allowed : 48.61 % Favored : 44.36 % Rotamer: Outliers : 15.44 % Allowed : 35.44 % Favored : 49.11 % Cbeta Deviations : 3.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 19.78 % 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: -8.17 (0.12), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.22 (0.09), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.041 0.006 HIS Z 13 PHE 0.178 0.016 PHE 7 19 TYR 0.065 0.006 TYR L 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6680.21 seconds wall clock time: 120 minutes 43.63 seconds (7243.63 seconds total)