Starting phenix.real_space_refine on Tue Sep 24 17:10:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/09_2024/3j89_6123.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/09_2024/3j89_6123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/09_2024/3j89_6123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/09_2024/3j89_6123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/09_2024/3j89_6123.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j89_6123/09_2024/3j89_6123.cif" } resolution = 3.6 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= 0.047 sd= 0.273 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 C 2755 2.51 5 N 855 2.21 5 O 817 1.98 5 H 4598 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9025 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 475 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R Time building chain proxies: 2.17, per 1000 atoms: 0.24 Number of scatterers: 9025 At special positions: 0 Unit cell: (90.78, 90.78, 67.32, 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) O 817 8.00 N 855 7.00 C 2755 6.00 H 4598 1.00 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: 2.55 Conformation dependent library (CDL) restraints added in 728.0 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 96.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 1 through 29 removed outlier: 3.543A pdb=" N ALA A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA C 7 " --> pdb=" O ARG C 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA D 7 " --> pdb=" O ARG D 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA H 7 " --> pdb=" O ARG H 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA J 7 " --> pdb=" O ARG J 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA K 7 " --> pdb=" O ARG K 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA L 7 " --> pdb=" O ARG L 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA M 7 " --> pdb=" O ARG M 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA N 7 " --> pdb=" O ARG N 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA O 7 " --> pdb=" O ARG O 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA P 7 " --> pdb=" O ARG P 3 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 29 removed outlier: 3.543A pdb=" N ALA Q 7 " --> pdb=" O ARG Q 3 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA R 7 " --> pdb=" O ARG R 3 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 29 removed outlier: 3.542A pdb=" N ALA S 7 " --> pdb=" O ARG S 3 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.08: 1102 1.08 - 1.19: 3496 1.19 - 1.31: 928 1.31 - 1.43: 1005 1.43 - 1.54: 2513 Bond restraints: 9044 Sorted by residual: bond pdb=" N ALA P 7 " pdb=" H ALA P 7 " ideal model delta sigma weight residual 0.860 1.032 -0.172 2.00e-02 2.50e+03 7.39e+01 bond pdb=" N ALA D 7 " pdb=" H ALA D 7 " ideal model delta sigma weight residual 0.860 1.032 -0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" N ALA J 7 " pdb=" H ALA J 7 " ideal model delta sigma weight residual 0.860 1.032 -0.172 2.00e-02 2.50e+03 7.35e+01 bond pdb=" N ALA E 7 " pdb=" H ALA E 7 " ideal model delta sigma weight residual 0.860 1.031 -0.171 2.00e-02 2.50e+03 7.35e+01 bond pdb=" N ALA F 7 " pdb=" H ALA F 7 " ideal model delta sigma weight residual 0.860 1.031 -0.171 2.00e-02 2.50e+03 7.35e+01 ... (remaining 9039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 12390 1.65 - 3.30: 2619 3.30 - 4.95: 588 4.95 - 6.60: 648 6.60 - 8.25: 95 Bond angle restraints: 16340 Sorted by residual: angle pdb=" N ILE R 4 " pdb=" CA ILE R 4 " pdb=" C ILE R 4 " ideal model delta sigma weight residual 112.83 108.63 4.20 9.90e-01 1.02e+00 1.80e+01 angle pdb=" N ILE C 4 " pdb=" CA ILE C 4 " pdb=" C ILE C 4 " ideal model delta sigma weight residual 112.83 108.67 4.16 9.90e-01 1.02e+00 1.76e+01 angle pdb=" N ILE Q 4 " pdb=" CA ILE Q 4 " pdb=" C ILE Q 4 " ideal model delta sigma weight residual 112.83 108.70 4.13 9.90e-01 1.02e+00 1.74e+01 angle pdb=" N ILE H 4 " pdb=" CA ILE H 4 " pdb=" C ILE H 4 " ideal model delta sigma weight residual 112.83 108.70 4.13 9.90e-01 1.02e+00 1.74e+01 angle pdb=" N ILE K 4 " pdb=" CA ILE K 4 " pdb=" C ILE K 4 " ideal model delta sigma weight residual 112.83 108.71 4.12 9.90e-01 1.02e+00 1.73e+01 ... (remaining 16335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.65: 3769 11.65 - 23.30: 221 23.30 - 34.95: 38 34.95 - 46.59: 19 46.59 - 58.24: 19 Dihedral angle restraints: 4066 sinusoidal: 2280 harmonic: 1786 Sorted by residual: dihedral pdb=" CA ILE C 4 " pdb=" C ILE C 4 " pdb=" N LEU C 5 " pdb=" CA LEU C 5 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE F 4 " pdb=" C ILE F 4 " pdb=" N LEU F 5 " pdb=" CA LEU F 5 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE O 4 " pdb=" C ILE O 4 " pdb=" N LEU O 5 " pdb=" CA LEU O 5 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 4063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 119 0.040 - 0.079: 197 0.079 - 0.118: 208 0.118 - 0.157: 109 0.157 - 0.197: 70 Chirality restraints: 703 Sorted by residual: chirality pdb=" CA GLU N 10 " pdb=" N GLU N 10 " pdb=" C GLU N 10 " pdb=" CB GLU N 10 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA GLU B 10 " pdb=" N GLU B 10 " pdb=" C GLU B 10 " pdb=" CB GLU B 10 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA GLU O 10 " pdb=" N GLU O 10 " pdb=" C GLU O 10 " pdb=" CB GLU O 10 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 700 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 22 " 0.020 2.00e-02 2.50e+03 3.11e-02 2.18e+01 pdb=" CG HIS E 22 " 0.025 2.00e-02 2.50e+03 pdb=" ND1 HIS E 22 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 HIS E 22 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS E 22 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS E 22 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 HIS E 22 " -0.071 2.00e-02 2.50e+03 pdb=" HD2 HIS E 22 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 HIS E 22 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 22 " 0.020 2.00e-02 2.50e+03 3.10e-02 2.17e+01 pdb=" CG HIS H 22 " 0.025 2.00e-02 2.50e+03 pdb=" ND1 HIS H 22 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 HIS H 22 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS H 22 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS H 22 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 HIS H 22 " -0.071 2.00e-02 2.50e+03 pdb=" HD2 HIS H 22 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 HIS H 22 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 22 " -0.019 2.00e-02 2.50e+03 3.10e-02 2.16e+01 pdb=" CG HIS R 22 " -0.025 2.00e-02 2.50e+03 pdb=" ND1 HIS R 22 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 HIS R 22 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS R 22 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS R 22 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 HIS R 22 " 0.070 2.00e-02 2.50e+03 pdb=" HD2 HIS R 22 " 0.025 2.00e-02 2.50e+03 pdb=" HE1 HIS R 22 " -0.018 2.00e-02 2.50e+03 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.29: 1304 2.29 - 2.84: 20083 2.84 - 3.40: 22086 3.40 - 3.95: 29734 3.95 - 4.50: 42641 Nonbonded interactions: 115848 Sorted by model distance: nonbonded pdb="HH22 ARG H 3 " pdb=" OE1 GLU H 6 " model vdw 1.738 2.450 nonbonded pdb="HH22 ARG S 3 " pdb=" OE1 GLU S 6 " model vdw 1.738 2.450 nonbonded pdb="HH22 ARG Q 3 " pdb=" OE1 GLU Q 6 " model vdw 1.738 2.450 nonbonded pdb="HH22 ARG N 3 " pdb=" OE1 GLU N 6 " model vdw 1.738 2.450 nonbonded pdb="HH22 ARG M 3 " pdb=" OE1 GLU M 6 " model vdw 1.738 2.450 ... (remaining 115843 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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 group one per residue 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: 0.050 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: 0.170 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 20.060 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 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 : 0.022 0.065 4446 Z= 1.471 Angle : 1.639 5.689 5985 Z= 1.159 Chirality : 0.101 0.197 703 Planarity : 0.010 0.046 798 Dihedral : 11.967 58.243 1710 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.29), residues: 513 helix: -0.44 (0.18), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 22 TYR 0.015 0.006 TYR F 15 ARG 0.003 0.001 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.733 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 outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.6408 time to fit residues: 103.3258 Evaluate side-chains 75 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4446 Z= 0.341 Angle : 0.675 5.492 5985 Z= 0.374 Chirality : 0.029 0.086 703 Planarity : 0.007 0.042 798 Dihedral : 4.874 16.651 646 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 2.51 % Allowed : 13.03 % Favored : 84.46 % 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: 2.79 (0.34), residues: 513 helix: 1.87 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 22 TYR 0.014 0.003 TYR E 15 ARG 0.008 0.002 ARG M 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.739 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: A 24 GLU cc_start: 0.7146 (tt0) cc_final: 0.6621 (tt0) REVERT: D 24 GLU cc_start: 0.7686 (tt0) cc_final: 0.7367 (tt0) REVERT: E 10 GLU cc_start: 0.7962 (tt0) cc_final: 0.7715 (tt0) REVERT: H 27 ARG cc_start: 0.7528 (mtt180) cc_final: 0.7306 (mtt180) REVERT: J 10 GLU cc_start: 0.8157 (tt0) cc_final: 0.7934 (mt-10) REVERT: Q 27 ARG cc_start: 0.7871 (mtp85) cc_final: 0.7631 (ttm-80) outliers start: 10 outliers final: 8 residues processed: 130 average time/residue: 0.6668 time to fit residues: 98.1366 Evaluate side-chains 110 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain N residue 8 ASP Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 26 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 11 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4446 Z= 0.179 Angle : 0.463 3.119 5985 Z= 0.271 Chirality : 0.028 0.105 703 Planarity : 0.004 0.027 798 Dihedral : 4.091 15.230 646 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 3.26 % Allowed : 20.05 % Favored : 76.69 % 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: 4.11 (0.34), residues: 513 helix: 2.68 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 22 TYR 0.010 0.002 TYR M 15 ARG 0.004 0.001 ARG M 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 0.726 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: I 10 GLU cc_start: 0.8075 (tt0) cc_final: 0.7828 (mt-10) REVERT: Q 10 GLU cc_start: 0.8352 (tt0) cc_final: 0.8080 (tt0) outliers start: 13 outliers final: 8 residues processed: 129 average time/residue: 0.6554 time to fit residues: 95.9391 Evaluate side-chains 119 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain R residue 25 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4446 Z= 0.391 Angle : 0.646 6.152 5985 Z= 0.376 Chirality : 0.032 0.093 703 Planarity : 0.007 0.043 798 Dihedral : 4.824 18.609 646 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.76 % Allowed : 20.80 % Favored : 74.44 % 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: 2.24 (0.34), residues: 513 helix: 1.53 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS P 22 TYR 0.022 0.005 TYR M 15 ARG 0.008 0.001 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7161 (mm-30) REVERT: I 10 GLU cc_start: 0.8105 (tt0) cc_final: 0.7881 (mt-10) REVERT: O 24 GLU cc_start: 0.7549 (tt0) cc_final: 0.7261 (tt0) REVERT: S 27 ARG cc_start: 0.7721 (ttm-80) cc_final: 0.7355 (ttm-80) outliers start: 19 outliers final: 14 residues processed: 96 average time/residue: 0.7086 time to fit residues: 76.8127 Evaluate side-chains 90 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 8 ASP Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 25 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4446 Z= 0.257 Angle : 0.519 4.462 5985 Z= 0.306 Chirality : 0.030 0.105 703 Planarity : 0.005 0.036 798 Dihedral : 4.442 16.791 646 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.51 % Allowed : 21.05 % Favored : 74.44 % 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: 2.97 (0.34), residues: 513 helix: 1.98 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 22 TYR 0.017 0.004 TYR M 15 ARG 0.005 0.001 ARG M 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.685 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: I 10 GLU cc_start: 0.8044 (tt0) cc_final: 0.7841 (mt-10) REVERT: N 27 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7613 (tpp80) outliers start: 18 outliers final: 17 residues processed: 96 average time/residue: 0.6994 time to fit residues: 75.5926 Evaluate side-chains 105 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 25 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4446 Z= 0.218 Angle : 0.478 3.994 5985 Z= 0.283 Chirality : 0.029 0.116 703 Planarity : 0.005 0.054 798 Dihedral : 4.302 20.839 646 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.76 % Allowed : 23.06 % Favored : 73.18 % 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: 3.47 (0.35), residues: 513 helix: 2.29 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS P 22 TYR 0.013 0.003 TYR M 15 ARG 0.009 0.001 ARG P 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 99 average time/residue: 0.7100 time to fit residues: 79.6392 Evaluate side-chains 105 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain R residue 25 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4446 Z= 0.383 Angle : 0.624 6.123 5985 Z= 0.366 Chirality : 0.033 0.151 703 Planarity : 0.007 0.037 798 Dihedral : 4.767 24.468 646 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.26 % Allowed : 23.31 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.35), residues: 513 helix: 1.41 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS P 22 TYR 0.021 0.005 TYR M 15 ARG 0.006 0.001 ARG I 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 24 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7384 (tt0) outliers start: 17 outliers final: 15 residues processed: 85 average time/residue: 0.7780 time to fit residues: 74.6360 Evaluate side-chains 89 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 25 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4446 Z= 0.292 Angle : 0.544 4.938 5985 Z= 0.321 Chirality : 0.031 0.166 703 Planarity : 0.006 0.032 798 Dihedral : 4.571 24.470 646 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.51 % Allowed : 23.56 % Favored : 71.93 % 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: 2.56 (0.35), residues: 513 helix: 1.73 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS P 22 TYR 0.016 0.004 TYR M 15 ARG 0.006 0.001 ARG L 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 15 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7135 (m-80) outliers start: 18 outliers final: 15 residues processed: 87 average time/residue: 0.7463 time to fit residues: 73.7032 Evaluate side-chains 93 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 25 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.6534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4446 Z= 0.242 Angle : 0.510 4.364 5985 Z= 0.300 Chirality : 0.030 0.148 703 Planarity : 0.005 0.028 798 Dihedral : 4.434 23.540 646 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.01 % Allowed : 24.81 % Favored : 71.18 % 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: 2.97 (0.35), residues: 513 helix: 1.98 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 22 TYR 0.014 0.004 TYR M 15 ARG 0.006 0.001 ARG L 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 16 residues processed: 92 average time/residue: 0.7343 time to fit residues: 76.8479 Evaluate side-chains 101 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.6582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4446 Z= 0.253 Angle : 0.523 4.399 5985 Z= 0.307 Chirality : 0.030 0.157 703 Planarity : 0.005 0.039 798 Dihedral : 4.453 25.464 646 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.51 % Allowed : 24.56 % Favored : 70.93 % 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: 2.92 (0.34), residues: 513 helix: 1.95 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS P 22 TYR 0.014 0.004 TYR M 15 ARG 0.006 0.001 ARG L 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 15 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7121 (m-80) outliers start: 18 outliers final: 17 residues processed: 94 average time/residue: 0.6889 time to fit residues: 73.4015 Evaluate side-chains 104 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 15 TYR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088614 restraints weight = 28534.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.091917 restraints weight = 14310.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.093992 restraints weight = 9947.040| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4446 Z= 0.243 Angle : 0.517 4.255 5985 Z= 0.304 Chirality : 0.030 0.150 703 Planarity : 0.005 0.030 798 Dihedral : 4.399 24.310 646 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.51 % Allowed : 24.56 % Favored : 70.93 % 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: 2.98 (0.34), residues: 513 helix: 1.98 (0.21), residues: 513 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 22 TYR 0.014 0.004 TYR M 15 ARG 0.005 0.001 ARG S 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2370.58 seconds wall clock time: 41 minutes 41.33 seconds (2501.33 seconds total)