Starting phenix.real_space_refine on Sun Mar 10 15:29:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az2_15730/03_2024/8az2_15730_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az2_15730/03_2024/8az2_15730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az2_15730/03_2024/8az2_15730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az2_15730/03_2024/8az2_15730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az2_15730/03_2024/8az2_15730_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az2_15730/03_2024/8az2_15730_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 3 Type Number sf(0) Gaussians C 1815 2.51 5 N 545 2.21 5 O 575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 11": "NH1" <-> "NH2" Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 11": "NH1" <-> "NH2" Residue "J PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2935 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "C" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "D" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "E" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "F" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "G" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "H" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "I" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "J" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "K" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "L" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "M" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "N" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "O" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Time building chain proxies: 1.87, per 1000 atoms: 0.64 Number of scatterers: 2935 At special positions: 0 Unit cell: (67.2, 93.24, 39.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 575 8.00 N 545 7.00 C 1815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 552.4 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 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: 0.39 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: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 470 1.29 - 1.35: 541 1.35 - 1.42: 361 1.42 - 1.48: 453 1.48 - 1.54: 1155 Bond restraints: 2980 Sorted by residual: bond pdb=" N GLY O 33 " pdb=" CA GLY O 33 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 7.09e-01 bond pdb=" N GLY F 33 " pdb=" CA GLY F 33 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.71e-01 bond pdb=" N GLY C 33 " pdb=" CA GLY C 33 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.30e-01 bond pdb=" N GLY L 33 " pdb=" CA GLY L 33 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.29e-01 bond pdb=" N GLY I 33 " pdb=" CA GLY I 33 " ideal model delta sigma weight residual 1.449 1.459 -0.010 1.45e-02 4.76e+03 4.99e-01 ... (remaining 2975 not shown) Histogram of bond angle deviations from ideal: 106.09 - 111.12: 1257 111.12 - 116.15: 615 116.15 - 121.18: 1232 121.18 - 126.21: 926 126.21 - 131.24: 15 Bond angle restraints: 4045 Sorted by residual: angle pdb=" NE ARG J 11 " pdb=" CZ ARG J 11 " pdb=" NH1 ARG J 11 " ideal model delta sigma weight residual 121.50 120.05 1.45 1.00e+00 1.00e+00 2.11e+00 angle pdb=" NE ARG G 11 " pdb=" CZ ARG G 11 " pdb=" NH1 ARG G 11 " ideal model delta sigma weight residual 121.50 120.07 1.43 1.00e+00 1.00e+00 2.05e+00 angle pdb=" N GLY N 20 " pdb=" CA GLY N 20 " pdb=" C GLY N 20 " ideal model delta sigma weight residual 113.48 115.56 -2.08 1.46e+00 4.69e-01 2.02e+00 angle pdb=" NE ARG F 11 " pdb=" CZ ARG F 11 " pdb=" NH1 ARG F 11 " ideal model delta sigma weight residual 121.50 120.10 1.40 1.00e+00 1.00e+00 1.97e+00 angle pdb=" N GLY E 20 " pdb=" CA GLY E 20 " pdb=" C GLY E 20 " ideal model delta sigma weight residual 113.48 115.53 -2.05 1.46e+00 4.69e-01 1.97e+00 ... (remaining 4040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.63: 1370 7.63 - 15.26: 200 15.26 - 22.90: 52 22.90 - 30.53: 8 30.53 - 38.16: 15 Dihedral angle restraints: 1645 sinusoidal: 550 harmonic: 1095 Sorted by residual: dihedral pdb=" CA SER K 19 " pdb=" C SER K 19 " pdb=" N GLY K 20 " pdb=" CA GLY K 20 " ideal model delta harmonic sigma weight residual 180.00 166.72 13.28 0 5.00e+00 4.00e-02 7.05e+00 dihedral pdb=" CA SER B 19 " pdb=" C SER B 19 " pdb=" N GLY B 20 " pdb=" CA GLY B 20 " ideal model delta harmonic sigma weight residual 180.00 166.76 13.24 0 5.00e+00 4.00e-02 7.01e+00 dihedral pdb=" CA SER E 19 " pdb=" C SER E 19 " pdb=" N GLY E 20 " pdb=" CA GLY E 20 " ideal model delta harmonic sigma weight residual 180.00 166.88 13.12 0 5.00e+00 4.00e-02 6.88e+00 ... (remaining 1642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 257 0.026 - 0.051: 124 0.051 - 0.077: 38 0.077 - 0.102: 31 0.102 - 0.128: 15 Chirality restraints: 465 Sorted by residual: chirality pdb=" CA ILE K 26 " pdb=" N ILE K 26 " pdb=" C ILE K 26 " pdb=" CB ILE K 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE F 26 " pdb=" N ILE F 26 " pdb=" C ILE F 26 " pdb=" CB ILE F 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE I 26 " pdb=" N ILE I 26 " pdb=" C ILE I 26 " pdb=" CB ILE I 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 462 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 28 " 0.002 2.00e-02 2.50e+03 3.97e-03 1.58e-01 pdb=" C SER B 28 " -0.007 2.00e-02 2.50e+03 pdb=" O SER B 28 " 0.003 2.00e-02 2.50e+03 pdb=" N SER B 29 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER K 28 " 0.002 2.00e-02 2.50e+03 3.74e-03 1.40e-01 pdb=" C SER K 28 " -0.006 2.00e-02 2.50e+03 pdb=" O SER K 28 " 0.002 2.00e-02 2.50e+03 pdb=" N SER K 29 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY K 20 " -0.002 2.00e-02 2.50e+03 3.66e-03 1.34e-01 pdb=" C GLY K 20 " 0.006 2.00e-02 2.50e+03 pdb=" O GLY K 20 " -0.002 2.00e-02 2.50e+03 pdb=" N ASN K 21 " -0.002 2.00e-02 2.50e+03 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1259 2.91 - 3.41: 2436 3.41 - 3.90: 5267 3.90 - 4.40: 5866 4.40 - 4.90: 10542 Nonbonded interactions: 25370 Sorted by model distance: nonbonded pdb=" O SER E 19 " pdb=" ND2 ASN E 21 " model vdw 2.412 2.520 nonbonded pdb=" O SER N 19 " pdb=" ND2 ASN N 21 " model vdw 2.412 2.520 nonbonded pdb=" O SER K 19 " pdb=" ND2 ASN K 21 " model vdw 2.424 2.520 nonbonded pdb=" O SER B 19 " pdb=" ND2 ASN B 21 " model vdw 2.424 2.520 nonbonded pdb=" O SER H 19 " pdb=" ND2 ASN H 21 " model vdw 2.447 2.520 ... (remaining 25365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 13 through 38) selection = chain 'B' selection = (chain 'C' and resid 13 through 38) selection = (chain 'D' and resid 13 through 38) selection = chain 'E' selection = (chain 'F' and resid 13 through 38) selection = (chain 'G' and resid 13 through 38) selection = chain 'H' selection = (chain 'I' and resid 13 through 38) selection = (chain 'J' and resid 13 through 38) selection = chain 'K' selection = (chain 'L' and resid 13 through 38) selection = (chain 'M' and resid 13 through 38) selection = chain 'N' selection = (chain 'O' and resid 13 through 38) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 5.380 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.630 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.010 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.003 0.016 2980 Z= 0.144 Angle : 0.451 3.082 4045 Z= 0.261 Chirality : 0.042 0.128 465 Planarity : 0.001 0.004 540 Dihedral : 9.018 38.160 945 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: -2.98 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 18 PHE 0.003 0.001 PHE H 15 TYR 0.003 0.001 TYR A 37 ARG 0.001 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.331 Fit side-chains REVERT: C 37 TYR cc_start: 0.8715 (m-80) cc_final: 0.8501 (m-80) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0892 time to fit residues: 2.5610 Evaluate side-chains 14 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.0970 chunk 8 optimal weight: 6.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 14 ASN ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 35 ASN D 35 ASN E 14 ASN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN F 35 ASN G 18 HIS G 35 ASN H 14 ASN ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN J 35 ASN K 14 ASN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 ASN M 35 ASN N 14 ASN ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 2980 Z= 0.313 Angle : 0.520 2.976 4045 Z= 0.298 Chirality : 0.047 0.131 465 Planarity : 0.003 0.015 540 Dihedral : 5.372 18.618 405 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.88 % Allowed : 3.75 % Favored : 94.38 % 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: -3.28 (0.25), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.19), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS J 18 PHE 0.010 0.002 PHE M 15 TYR 0.011 0.002 TYR A 37 ARG 0.002 0.000 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 10 time to evaluate : 0.301 Fit side-chains REVERT: D 31 ASN cc_start: 0.8478 (t0) cc_final: 0.8102 (t0) outliers start: 6 outliers final: 4 residues processed: 16 average time/residue: 0.0744 time to fit residues: 2.0511 Evaluate side-chains 14 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 10 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2980 Z= 0.100 Angle : 0.409 3.540 4045 Z= 0.227 Chirality : 0.044 0.126 465 Planarity : 0.001 0.007 540 Dihedral : 4.258 15.381 405 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.25 % Allowed : 6.88 % Favored : 91.88 % 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: -3.28 (0.25), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.19), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 18 PHE 0.014 0.001 PHE O 23 TYR 0.008 0.001 TYR D 37 ARG 0.000 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 9 time to evaluate : 0.338 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 13 average time/residue: 0.0951 time to fit residues: 2.1538 Evaluate side-chains 13 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 9 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2980 Z= 0.099 Angle : 0.386 3.246 4045 Z= 0.217 Chirality : 0.043 0.125 465 Planarity : 0.001 0.006 540 Dihedral : 4.021 14.686 405 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.25 % Allowed : 9.38 % Favored : 89.38 % 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: -3.29 (0.26), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.20), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 18 PHE 0.010 0.001 PHE L 23 TYR 0.007 0.001 TYR D 37 ARG 0.000 0.000 ARG O 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 9 time to evaluate : 0.296 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 13 average time/residue: 0.0813 time to fit residues: 1.8318 Evaluate side-chains 13 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 9 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2980 Z= 0.146 Angle : 0.395 3.235 4045 Z= 0.226 Chirality : 0.044 0.128 465 Planarity : 0.002 0.008 540 Dihedral : 4.280 15.495 405 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.25 % Allowed : 10.31 % Favored : 88.44 % 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: -3.30 (0.26), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.20), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 18 PHE 0.011 0.001 PHE I 23 TYR 0.007 0.001 TYR D 37 ARG 0.001 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 10 time to evaluate : 0.324 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 14 average time/residue: 0.0870 time to fit residues: 2.1111 Evaluate side-chains 14 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 10 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2980 Z= 0.160 Angle : 0.406 3.456 4045 Z= 0.233 Chirality : 0.044 0.130 465 Planarity : 0.002 0.010 540 Dihedral : 4.414 15.767 405 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.25 % Allowed : 10.62 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.26), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.20), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS M 18 PHE 0.010 0.001 PHE L 23 TYR 0.007 0.001 TYR D 37 ARG 0.001 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 10 time to evaluate : 0.321 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 14 average time/residue: 0.0839 time to fit residues: 2.0292 Evaluate side-chains 14 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 10 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2980 Z= 0.099 Angle : 0.375 3.463 4045 Z= 0.213 Chirality : 0.043 0.127 465 Planarity : 0.001 0.006 540 Dihedral : 4.032 14.602 405 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.25 % Allowed : 10.62 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.20), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 18 PHE 0.010 0.001 PHE L 23 TYR 0.006 0.001 TYR D 37 ARG 0.000 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 9 time to evaluate : 0.326 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 13 average time/residue: 0.0893 time to fit residues: 2.0018 Evaluate side-chains 13 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 9 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.0980 chunk 22 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2980 Z= 0.092 Angle : 0.367 3.399 4045 Z= 0.209 Chirality : 0.043 0.126 465 Planarity : 0.001 0.005 540 Dihedral : 3.914 14.702 405 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.25 % Allowed : 10.94 % Favored : 87.81 % 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: -3.31 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 18 PHE 0.011 0.001 PHE L 23 TYR 0.006 0.001 TYR D 37 ARG 0.000 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 11 time to evaluate : 0.338 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 15 average time/residue: 0.0850 time to fit residues: 2.1777 Evaluate side-chains 15 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 11 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2980 Z= 0.268 Angle : 0.449 3.471 4045 Z= 0.261 Chirality : 0.045 0.131 465 Planarity : 0.003 0.012 540 Dihedral : 4.908 17.036 405 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.25 % Allowed : 11.56 % Favored : 87.19 % 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: -3.49 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 18 PHE 0.012 0.002 PHE L 23 TYR 0.009 0.002 TYR J 37 ARG 0.001 0.000 ARG O 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.333 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 22 average time/residue: 0.0781 time to fit residues: 2.8113 Evaluate side-chains 22 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2980 Z= 0.172 Angle : 0.408 3.699 4045 Z= 0.234 Chirality : 0.044 0.133 465 Planarity : 0.002 0.008 540 Dihedral : 4.520 15.186 405 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.25 % Allowed : 12.50 % Favored : 86.25 % 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: -3.55 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.20), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 18 PHE 0.012 0.001 PHE L 23 TYR 0.007 0.001 TYR D 37 ARG 0.001 0.000 ARG C 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 15 time to evaluate : 0.302 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 19 average time/residue: 0.0791 time to fit residues: 2.5068 Evaluate side-chains 19 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 15 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.073919 restraints weight = 3064.937| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.85 r_work: 0.3004 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2980 Z= 0.243 Angle : 0.444 3.738 4045 Z= 0.257 Chirality : 0.045 0.133 465 Planarity : 0.002 0.012 540 Dihedral : 4.928 16.600 405 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.25 % Allowed : 12.81 % Favored : 85.94 % 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: -3.60 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.20), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 18 PHE 0.012 0.002 PHE C 23 TYR 0.012 0.002 TYR I 37 ARG 0.001 0.000 ARG C 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1025.42 seconds wall clock time: 19 minutes 24.31 seconds (1164.31 seconds total)