Starting phenix.real_space_refine on Sun Mar 10 18:43:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az3_15731/03_2024/8az3_15731_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az3_15731/03_2024/8az3_15731.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/8az3_15731/03_2024/8az3_15731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az3_15731/03_2024/8az3_15731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az3_15731/03_2024/8az3_15731_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az3_15731/03_2024/8az3_15731_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= 0.003 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 2500 2.51 5 N 760 2.21 5 O 780 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 "B ARG 11": "NH1" <-> "NH2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 11": "NH1" <-> "NH2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 11": "NH1" <-> "NH2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 23": "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 "K PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 15": "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 "N ARG 11": "NH1" <-> "NH2" Residue "N PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 11": "NH1" <-> "NH2" Residue "Q PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 11": "NH1" <-> "NH2" Residue "R PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 15": "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: 4040 Number of models: 1 Model: "" Number of chains: 20 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: 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: "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: 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: "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: 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: "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: 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: "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: 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: "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} Chain: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: 2.40, per 1000 atoms: 0.59 Number of scatterers: 4040 At special positions: 0 Unit cell: (91.56, 101.64, 42, 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 780 8.00 N 760 7.00 C 2500 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: 1.50 Conformation dependent library (CDL) restraints added in 839.2 milliseconds 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 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: 0.47 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: 1.63 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: 640 1.29 - 1.36: 760 1.36 - 1.42: 500 1.42 - 1.48: 540 1.48 - 1.55: 1660 Bond restraints: 4100 Sorted by residual: bond pdb=" N VAL O 32 " pdb=" CA VAL O 32 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.29e-02 6.01e+03 7.08e+00 bond pdb=" N VAL L 32 " pdb=" CA VAL L 32 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.29e-02 6.01e+03 7.07e+00 bond pdb=" N VAL D 32 " pdb=" CA VAL D 32 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.29e-02 6.01e+03 7.05e+00 bond pdb=" N VAL C 32 " pdb=" CA VAL C 32 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.29e-02 6.01e+03 6.96e+00 bond pdb=" N VAL K 32 " pdb=" CA VAL K 32 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.29e-02 6.01e+03 6.92e+00 ... (remaining 4095 not shown) Histogram of bond angle deviations from ideal: 106.03 - 111.09: 1645 111.09 - 116.15: 944 116.15 - 121.22: 1755 121.22 - 126.28: 1196 126.28 - 131.34: 20 Bond angle restraints: 5560 Sorted by residual: angle pdb=" CA ASN K 31 " pdb=" C ASN K 31 " pdb=" O ASN K 31 " ideal model delta sigma weight residual 120.33 117.66 2.67 1.08e+00 8.57e-01 6.12e+00 angle pdb=" CA ASN G 31 " pdb=" C ASN G 31 " pdb=" O ASN G 31 " ideal model delta sigma weight residual 120.33 117.73 2.60 1.08e+00 8.57e-01 5.81e+00 angle pdb=" CA ASN C 31 " pdb=" C ASN C 31 " pdb=" O ASN C 31 " ideal model delta sigma weight residual 120.33 117.73 2.60 1.08e+00 8.57e-01 5.81e+00 angle pdb=" CA ASN O 31 " pdb=" C ASN O 31 " pdb=" O ASN O 31 " ideal model delta sigma weight residual 120.33 117.73 2.60 1.08e+00 8.57e-01 5.80e+00 angle pdb=" CA ILE O 26 " pdb=" C ILE O 26 " pdb=" O ILE O 26 " ideal model delta sigma weight residual 120.48 117.84 2.64 1.10e+00 8.26e-01 5.78e+00 ... (remaining 5555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.53: 1970 8.53 - 17.07: 183 17.07 - 25.60: 77 25.60 - 34.14: 40 34.14 - 42.67: 10 Dihedral angle restraints: 2280 sinusoidal: 780 harmonic: 1500 Sorted by residual: dihedral pdb=" N HIS F 18 " pdb=" CA HIS F 18 " pdb=" CB HIS F 18 " pdb=" CG HIS F 18 " ideal model delta sinusoidal sigma weight residual -60.00 -89.44 29.44 3 1.50e+01 4.44e-03 4.60e+00 dihedral pdb=" N HIS N 18 " pdb=" CA HIS N 18 " pdb=" CB HIS N 18 " pdb=" CG HIS N 18 " ideal model delta sinusoidal sigma weight residual -60.00 -89.43 29.43 3 1.50e+01 4.44e-03 4.60e+00 dihedral pdb=" N HIS I 18 " pdb=" CA HIS I 18 " pdb=" CB HIS I 18 " pdb=" CG HIS I 18 " ideal model delta sinusoidal sigma weight residual -60.00 -89.43 29.43 3 1.50e+01 4.44e-03 4.60e+00 ... (remaining 2277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 467 0.049 - 0.098: 96 0.098 - 0.147: 57 0.147 - 0.196: 10 0.196 - 0.245: 10 Chirality restraints: 640 Sorted by residual: chirality pdb=" CA ILE P 26 " pdb=" N ILE P 26 " pdb=" C ILE P 26 " pdb=" CB ILE P 26 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.50e+00 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 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE D 26 " pdb=" N ILE D 26 " pdb=" C ILE D 26 " pdb=" CB ILE D 26 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 637 not shown) Planarity restraints: 740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR L 30 " 0.004 2.00e-02 2.50e+03 8.87e-03 7.88e-01 pdb=" C THR L 30 " -0.015 2.00e-02 2.50e+03 pdb=" O THR L 30 " 0.006 2.00e-02 2.50e+03 pdb=" N ASN L 31 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR O 30 " -0.004 2.00e-02 2.50e+03 8.82e-03 7.78e-01 pdb=" C THR O 30 " 0.015 2.00e-02 2.50e+03 pdb=" O THR O 30 " -0.006 2.00e-02 2.50e+03 pdb=" N ASN O 31 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR P 30 " 0.004 2.00e-02 2.50e+03 8.71e-03 7.59e-01 pdb=" C THR P 30 " -0.015 2.00e-02 2.50e+03 pdb=" O THR P 30 " 0.006 2.00e-02 2.50e+03 pdb=" N ASN P 31 " 0.005 2.00e-02 2.50e+03 ... (remaining 737 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2155 2.99 - 3.47: 3580 3.47 - 3.94: 7138 3.94 - 4.42: 7927 4.42 - 4.90: 13831 Nonbonded interactions: 34631 Sorted by model distance: nonbonded pdb=" O LEU K 12 " pdb=" N ALA O 13 " model vdw 2.509 2.520 nonbonded pdb=" N LEU K 12 " pdb=" O ARG O 11 " model vdw 2.530 2.520 nonbonded pdb=" N ASN K 14 " pdb=" O ALA O 13 " model vdw 2.576 2.520 nonbonded pdb=" O ASN K 14 " pdb=" N PHE O 15 " model vdw 2.610 2.520 nonbonded pdb=" O VAL K 32 " pdb=" N GLY O 33 " model vdw 2.612 2.520 ... (remaining 34626 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 1.470 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: 5.520 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.590 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.005 0.037 4100 Z= 0.365 Angle : 0.656 3.136 5560 Z= 0.459 Chirality : 0.060 0.245 640 Planarity : 0.002 0.009 740 Dihedral : 9.595 42.670 1320 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.88 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 18 PHE 0.003 0.001 PHE F 23 TYR 0.008 0.001 TYR O 37 ARG 0.001 0.000 ARG R 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.453 Fit side-chains REVERT: J 31 ASN cc_start: 0.8531 (t0) cc_final: 0.8278 (t0) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0897 time to fit residues: 6.9161 Evaluate side-chains 50 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 ASN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN H 35 ASN I 14 ASN ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN L 35 ASN M 14 ASN M 22 ASN ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 ASN N 22 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 ASN P 35 ASN Q 22 ASN R 22 ASN S 35 ASN T 35 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4100 Z= 0.236 Angle : 0.484 4.935 5560 Z= 0.271 Chirality : 0.045 0.136 640 Planarity : 0.002 0.010 740 Dihedral : 5.268 16.382 560 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.23 % Allowed : 2.95 % Favored : 96.82 % 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: -3.46 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS A 18 PHE 0.010 0.002 PHE A 15 TYR 0.013 0.003 TYR O 37 ARG 0.001 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.440 Fit side-chains REVERT: T 23 PHE cc_start: 0.7933 (m-80) cc_final: 0.7639 (m-80) outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.0927 time to fit residues: 5.6977 Evaluate side-chains 40 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 29 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 40.0000 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 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: 0.8006 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 : 0.004 0.024 4100 Z= 0.198 Angle : 0.450 3.150 5560 Z= 0.256 Chirality : 0.044 0.123 640 Planarity : 0.002 0.008 740 Dihedral : 5.217 17.586 560 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.91 % Allowed : 5.45 % Favored : 93.64 % 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: -3.87 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS Q 18 PHE 0.009 0.001 PHE D 23 TYR 0.015 0.003 TYR R 37 ARG 0.001 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.444 Fit side-chains REVERT: S 18 HIS cc_start: 0.7717 (t-170) cc_final: 0.7455 (t-90) REVERT: T 23 PHE cc_start: 0.7878 (m-80) cc_final: 0.7450 (m-80) outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.0914 time to fit residues: 5.5901 Evaluate side-chains 41 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain R residue 29 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN D 31 ASN E 14 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN H 31 ASN I 14 ASN ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 ASN ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN L 31 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN Q 14 ASN ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 14 ASN S 31 ASN T 31 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 4100 Z= 0.337 Angle : 0.535 3.164 5560 Z= 0.307 Chirality : 0.047 0.123 640 Planarity : 0.003 0.011 740 Dihedral : 5.959 20.058 560 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.82 % Allowed : 9.09 % Favored : 89.09 % 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: -4.20 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS Q 18 PHE 0.010 0.002 PHE B 23 TYR 0.017 0.003 TYR O 37 ARG 0.001 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.408 Fit side-chains REVERT: O 18 HIS cc_start: 0.7456 (t-170) cc_final: 0.7189 (t-90) outliers start: 8 outliers final: 7 residues processed: 45 average time/residue: 0.0866 time to fit residues: 6.0516 Evaluate side-chains 52 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain R residue 29 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4100 Z= 0.152 Angle : 0.439 3.409 5560 Z= 0.245 Chirality : 0.043 0.127 640 Planarity : 0.002 0.006 740 Dihedral : 5.003 15.570 560 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.36 % Allowed : 10.23 % Favored : 88.41 % 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: -4.33 (0.21), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.16), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS Q 18 PHE 0.009 0.001 PHE D 23 TYR 0.013 0.002 TYR R 37 ARG 0.001 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.461 Fit side-chains REVERT: T 23 PHE cc_start: 0.7962 (m-80) cc_final: 0.7575 (m-80) outliers start: 6 outliers final: 6 residues processed: 45 average time/residue: 0.0839 time to fit residues: 5.9380 Evaluate side-chains 49 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain R residue 29 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 8.9990 chunk 38 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 4100 Z= 0.369 Angle : 0.574 3.124 5560 Z= 0.326 Chirality : 0.048 0.123 640 Planarity : 0.004 0.012 740 Dihedral : 5.962 19.988 560 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.05 % Allowed : 11.82 % Favored : 86.14 % 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: -4.64 (0.21), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.16), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS Q 18 PHE 0.011 0.002 PHE L 15 TYR 0.018 0.004 TYR O 37 ARG 0.001 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.441 Fit side-chains REVERT: D 37 TYR cc_start: 0.7397 (p90) cc_final: 0.6797 (p90) REVERT: T 23 PHE cc_start: 0.8028 (m-80) cc_final: 0.7648 (m-80) outliers start: 9 outliers final: 9 residues processed: 54 average time/residue: 0.0874 time to fit residues: 7.1585 Evaluate side-chains 58 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain R residue 29 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4100 Z= 0.171 Angle : 0.460 3.496 5560 Z= 0.256 Chirality : 0.044 0.126 640 Planarity : 0.002 0.006 740 Dihedral : 5.047 15.954 560 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.05 % Allowed : 14.09 % Favored : 83.86 % 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: -4.61 (0.20), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.16), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS Q 18 PHE 0.011 0.001 PHE D 23 TYR 0.014 0.003 TYR L 37 ARG 0.001 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.464 Fit side-chains REVERT: D 37 TYR cc_start: 0.7250 (p90) cc_final: 0.6859 (p90) REVERT: T 23 PHE cc_start: 0.8039 (m-80) cc_final: 0.7616 (m-80) outliers start: 9 outliers final: 8 residues processed: 51 average time/residue: 0.0921 time to fit residues: 7.2475 Evaluate side-chains 57 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain S residue 35 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 30.0000 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 30.0000 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 4100 Z= 0.256 Angle : 0.504 3.243 5560 Z= 0.282 Chirality : 0.045 0.122 640 Planarity : 0.002 0.009 740 Dihedral : 5.347 18.461 560 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 2.27 % Allowed : 13.86 % Favored : 83.86 % 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: -4.63 (0.21), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.16), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 18 PHE 0.013 0.001 PHE D 23 TYR 0.016 0.003 TYR L 37 ARG 0.001 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.406 Fit side-chains REVERT: D 37 TYR cc_start: 0.7224 (p90) cc_final: 0.6932 (p90) REVERT: T 23 PHE cc_start: 0.8043 (m-80) cc_final: 0.7640 (m-80) outliers start: 10 outliers final: 10 residues processed: 50 average time/residue: 0.0822 time to fit residues: 6.3090 Evaluate side-chains 55 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain S residue 35 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 4100 Z= 0.085 Angle : 0.424 3.615 5560 Z= 0.233 Chirality : 0.043 0.128 640 Planarity : 0.001 0.007 740 Dihedral : 4.475 14.038 560 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.59 % Allowed : 14.55 % Favored : 83.86 % 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: -4.56 (0.21), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.16), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Q 18 PHE 0.013 0.001 PHE D 23 TYR 0.012 0.002 TYR C 37 ARG 0.000 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.477 Fit side-chains REVERT: T 23 PHE cc_start: 0.7996 (m-80) cc_final: 0.7602 (m-80) outliers start: 7 outliers final: 7 residues processed: 48 average time/residue: 0.0862 time to fit residues: 6.4509 Evaluate side-chains 53 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain S residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 0.2980 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4100 Z= 0.238 Angle : 0.486 3.168 5560 Z= 0.273 Chirality : 0.044 0.120 640 Planarity : 0.002 0.013 740 Dihedral : 5.170 18.269 560 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.59 % Allowed : 14.32 % Favored : 84.09 % 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: -4.61 (0.21), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.16), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 18 PHE 0.014 0.001 PHE P 15 TYR 0.032 0.003 TYR D 37 ARG 0.001 0.000 ARG F 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.507 Fit side-chains REVERT: T 23 PHE cc_start: 0.8064 (m-80) cc_final: 0.7647 (m-80) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.0845 time to fit residues: 6.4288 Evaluate side-chains 53 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain R residue 29 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.131535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.082841 restraints weight = 4367.416| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.57 r_work: 0.3248 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 4100 Z= 0.320 Angle : 0.550 3.559 5560 Z= 0.308 Chirality : 0.046 0.119 640 Planarity : 0.003 0.016 740 Dihedral : 5.613 18.523 560 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 1.36 % Allowed : 14.32 % Favored : 84.32 % 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: -4.69 (0.21), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.16), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS Q 18 PHE 0.014 0.002 PHE D 23 TYR 0.038 0.004 TYR D 37 ARG 0.002 0.000 ARG F 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1105.29 seconds wall clock time: 20 minutes 46.52 seconds (1246.52 seconds total)