Starting phenix.real_space_refine on Sun Mar 10 18:25:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/03_2024/6zrq_11382_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/03_2024/6zrq_11382.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/03_2024/6zrq_11382_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/03_2024/6zrq_11382_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/03_2024/6zrq_11382_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/03_2024/6zrq_11382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/03_2024/6zrq_11382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/03_2024/6zrq_11382_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/03_2024/6zrq_11382_trim_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 1272 2.51 5 N 360 2.21 5 O 408 1.98 5 H 1776 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 3816 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "B" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "C" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "D" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "E" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "F" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "G" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "H" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "I" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "J" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "K" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "L" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Time building chain proxies: 1.93, per 1000 atoms: 0.51 Number of scatterers: 3816 At special positions: 0 Unit cell: (50.055, 79.875, 44.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 408 8.00 N 360 7.00 C 1272 6.00 H 1776 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 3.26 Conformation dependent library (CDL) restraints added in 555.9 milliseconds 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 480 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: 0.55 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: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 0.97: 1741 0.97 - 1.12: 35 1.12 - 1.26: 324 1.26 - 1.40: 612 1.40 - 1.54: 1140 Bond restraints: 3852 Sorted by residual: bond pdb=" C TYC F 37 " pdb=" NXT TYC F 37 " ideal model delta sigma weight residual 1.451 1.330 0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" C TYC B 37 " pdb=" NXT TYC B 37 " ideal model delta sigma weight residual 1.451 1.330 0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" C TYC H 37 " pdb=" NXT TYC H 37 " ideal model delta sigma weight residual 1.451 1.330 0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" C TYC G 37 " pdb=" NXT TYC G 37 " ideal model delta sigma weight residual 1.451 1.330 0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" C TYC C 37 " pdb=" NXT TYC C 37 " ideal model delta sigma weight residual 1.451 1.330 0.121 2.00e-02 2.50e+03 3.64e+01 ... (remaining 3847 not shown) Histogram of bond angle deviations from ideal: 103.47 - 108.96: 1698 108.96 - 114.46: 2726 114.46 - 119.96: 762 119.96 - 125.45: 1486 125.45 - 130.95: 84 Bond angle restraints: 6756 Sorted by residual: angle pdb=" CA LEU I 16 " pdb=" CB LEU I 16 " pdb=" CG LEU I 16 " ideal model delta sigma weight residual 116.30 128.07 -11.77 3.50e+00 8.16e-02 1.13e+01 angle pdb=" CA LEU K 16 " pdb=" CB LEU K 16 " pdb=" CG LEU K 16 " ideal model delta sigma weight residual 116.30 128.05 -11.75 3.50e+00 8.16e-02 1.13e+01 angle pdb=" CA LEU C 16 " pdb=" CB LEU C 16 " pdb=" CG LEU C 16 " ideal model delta sigma weight residual 116.30 128.04 -11.74 3.50e+00 8.16e-02 1.13e+01 angle pdb=" CA LEU D 16 " pdb=" CB LEU D 16 " pdb=" CG LEU D 16 " ideal model delta sigma weight residual 116.30 128.03 -11.73 3.50e+00 8.16e-02 1.12e+01 angle pdb=" CA LEU F 16 " pdb=" CB LEU F 16 " pdb=" CG LEU F 16 " ideal model delta sigma weight residual 116.30 128.03 -11.73 3.50e+00 8.16e-02 1.12e+01 ... (remaining 6751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.47: 1416 12.47 - 24.93: 312 24.93 - 37.40: 24 37.40 - 49.86: 36 49.86 - 62.33: 60 Dihedral angle restraints: 1848 sinusoidal: 948 harmonic: 900 Sorted by residual: dihedral pdb=" CA SER D 19 " pdb=" C SER D 19 " pdb=" N GLY D 20 " pdb=" CA GLY D 20 " ideal model delta harmonic sigma weight residual 180.00 153.81 26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA SER H 19 " pdb=" C SER H 19 " pdb=" N GLY H 20 " pdb=" CA GLY H 20 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 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 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 1845 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.031: 141 0.031 - 0.058: 75 0.058 - 0.085: 84 0.085 - 0.112: 12 0.112 - 0.139: 12 Chirality restraints: 324 Sorted by residual: chirality pdb=" CA TYC H 37 " pdb=" N TYC H 37 " pdb=" C TYC H 37 " pdb=" CB TYC H 37 " both_signs ideal model delta sigma weight residual False 2.61 2.47 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA TYC J 37 " pdb=" N TYC J 37 " pdb=" C TYC J 37 " pdb=" CB TYC J 37 " both_signs ideal model delta sigma weight residual False 2.61 2.47 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA TYC A 37 " pdb=" N TYC A 37 " pdb=" C TYC A 37 " pdb=" CB TYC A 37 " both_signs ideal model delta sigma weight residual False 2.61 2.47 0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 321 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS K 18 " -0.001 2.00e-02 2.50e+03 6.31e-03 8.96e-01 pdb=" CG HIS K 18 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS K 18 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS K 18 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS K 18 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS K 18 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 HIS K 18 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS K 18 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 HIS K 18 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS L 18 " 0.001 2.00e-02 2.50e+03 6.28e-03 8.88e-01 pdb=" CG HIS L 18 " 0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS L 18 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS L 18 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS L 18 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS L 18 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 HIS L 18 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS L 18 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 HIS L 18 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 18 " -0.001 2.00e-02 2.50e+03 6.22e-03 8.70e-01 pdb=" CG HIS E 18 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS E 18 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS E 18 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS E 18 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS E 18 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 HIS E 18 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS E 18 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 HIS E 18 " -0.001 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.40: 1684 2.40 - 2.92: 8524 2.92 - 3.45: 8486 3.45 - 3.97: 12777 3.97 - 4.50: 16874 Nonbonded interactions: 48345 Sorted by model distance: nonbonded pdb=" HA THR J 36 " pdb="HG23 THR L 36 " model vdw 1.869 2.440 nonbonded pdb=" HG SER E 29 " pdb=" H THR E 30 " model vdw 1.884 2.100 nonbonded pdb=" HG SER G 29 " pdb=" H THR G 30 " model vdw 1.884 2.100 nonbonded pdb=" HG SER F 29 " pdb=" H THR F 30 " model vdw 1.884 2.100 nonbonded pdb=" HG SER I 29 " pdb=" H THR I 30 " model vdw 1.884 2.100 ... (remaining 48340 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.070 Extract box with map and model: 5.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.460 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 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 : 0.014 0.121 2076 Z= 0.643 Angle : 1.451 11.770 2820 Z= 0.588 Chirality : 0.052 0.139 324 Planarity : 0.004 0.008 372 Dihedral : 14.334 52.051 636 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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: -4.20 (0.39), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.30), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.007 HIS K 18 PHE 0.008 0.004 PHE A 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 16 LEU cc_start: 0.6021 (pt) cc_final: 0.5466 (pt) REVERT: J 16 LEU cc_start: 0.6379 (pt) cc_final: 0.6177 (pt) REVERT: K 36 THR cc_start: 0.7643 (t) cc_final: 0.7433 (t) REVERT: L 36 THR cc_start: 0.7117 (t) cc_final: 0.6914 (t) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1281 time to fit residues: 10.7660 Evaluate side-chains 20 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2076 Z= 0.128 Angle : 0.623 5.497 2820 Z= 0.317 Chirality : 0.050 0.150 324 Planarity : 0.002 0.007 372 Dihedral : 13.769 59.808 300 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.31 % Allowed : 20.37 % Favored : 77.31 % 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: -4.26 (0.38), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.29), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 18 PHE 0.015 0.002 PHE H 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 37 average time/residue: 0.1300 time to fit residues: 6.6868 Evaluate side-chains 24 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain I residue 21 ASN Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain L residue 21 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2076 Z= 0.121 Angle : 0.558 5.099 2820 Z= 0.289 Chirality : 0.047 0.141 324 Planarity : 0.002 0.006 372 Dihedral : 11.569 59.414 300 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.39 % Allowed : 25.93 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.29), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.22), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 18 PHE 0.008 0.001 PHE C 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.1268 time to fit residues: 4.1193 Evaluate side-chains 18 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain L residue 21 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2076 Z= 0.154 Angle : 0.600 6.057 2820 Z= 0.306 Chirality : 0.049 0.161 324 Planarity : 0.002 0.007 372 Dihedral : 10.401 42.031 300 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.24 % Allowed : 26.85 % Favored : 69.91 % 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: -5.32 (0.28), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.21), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 18 PHE 0.014 0.002 PHE F 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 9 time to evaluate : 0.297 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 15 average time/residue: 0.1044 time to fit residues: 2.5046 Evaluate side-chains 14 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 8 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain L residue 21 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2076 Z= 0.098 Angle : 0.494 4.274 2820 Z= 0.259 Chirality : 0.047 0.131 324 Planarity : 0.002 0.005 372 Dihedral : 10.344 46.253 300 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.24 % Allowed : 28.24 % Favored : 68.52 % 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: -5.28 (0.30), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.23), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS K 18 PHE 0.007 0.001 PHE F 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 12 time to evaluate : 0.326 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 19 average time/residue: 0.1005 time to fit residues: 3.1606 Evaluate side-chains 15 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 12 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain J residue 35 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.6323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2076 Z= 0.115 Angle : 0.506 4.416 2820 Z= 0.265 Chirality : 0.048 0.136 324 Planarity : 0.002 0.005 372 Dihedral : 9.458 43.530 300 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 2.78 % Allowed : 28.70 % Favored : 68.52 % 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: -5.34 (0.31), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.24), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 18 PHE 0.008 0.001 PHE F 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 13 time to evaluate : 0.330 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 19 average time/residue: 0.0994 time to fit residues: 3.0015 Evaluate side-chains 16 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 12 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 15 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.6636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2076 Z= 0.111 Angle : 0.488 4.023 2820 Z= 0.260 Chirality : 0.047 0.130 324 Planarity : 0.002 0.004 372 Dihedral : 8.761 42.965 300 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % Rotamer: Outliers : 2.78 % Allowed : 29.63 % Favored : 67.59 % 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: -5.46 (0.31), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.15 (0.24), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS K 18 PHE 0.008 0.001 PHE F 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 11 time to evaluate : 0.342 Fit side-chains REVERT: I 15 PHE cc_start: 0.3793 (OUTLIER) cc_final: 0.2558 (m-80) outliers start: 6 outliers final: 3 residues processed: 17 average time/residue: 0.1052 time to fit residues: 2.9250 Evaluate side-chains 15 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 11 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain I residue 15 PHE Chi-restraints excluded: chain J residue 15 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.6886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2076 Z= 0.107 Angle : 0.465 3.827 2820 Z= 0.252 Chirality : 0.046 0.128 324 Planarity : 0.002 0.004 372 Dihedral : 8.191 41.790 300 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.75 % Favored : 86.25 % Rotamer: Outliers : 2.78 % Allowed : 28.70 % Favored : 68.52 % 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: -5.49 (0.31), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.18 (0.24), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 18 PHE 0.007 0.001 PHE F 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 11 time to evaluate : 0.323 Fit side-chains REVERT: I 15 PHE cc_start: 0.3704 (OUTLIER) cc_final: 0.2220 (m-80) outliers start: 6 outliers final: 5 residues processed: 15 average time/residue: 0.1099 time to fit residues: 2.6718 Evaluate side-chains 17 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 11 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain I residue 15 PHE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 2076 Z= 0.120 Angle : 0.463 3.915 2820 Z= 0.255 Chirality : 0.046 0.128 324 Planarity : 0.002 0.004 372 Dihedral : 8.097 38.235 300 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 1.85 % Allowed : 29.17 % Favored : 68.98 % 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: -5.63 (0.30), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.28 (0.23), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS K 18 PHE 0.008 0.001 PHE F 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.329 Fit side-chains REVERT: I 15 PHE cc_start: 0.3334 (OUTLIER) cc_final: 0.2021 (m-80) outliers start: 4 outliers final: 2 residues processed: 16 average time/residue: 0.1163 time to fit residues: 2.9097 Evaluate side-chains 16 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 13 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain I residue 15 PHE Chi-restraints excluded: chain J residue 15 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 chunk 14 optimal weight: 0.5980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2076 Z= 0.081 Angle : 0.423 3.387 2820 Z= 0.235 Chirality : 0.045 0.119 324 Planarity : 0.001 0.004 372 Dihedral : 8.100 40.311 300 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 1.39 % Allowed : 29.63 % Favored : 68.98 % 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: -5.53 (0.31), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.24), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS K 18 PHE 0.009 0.001 PHE F 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 13 time to evaluate : 0.283 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 15 average time/residue: 0.1005 time to fit residues: 2.4931 Evaluate side-chains 16 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 13 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain I residue 15 PHE Chi-restraints excluded: chain J residue 15 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.0470 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 18 HIS ** 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 = 0.4263 r_free = 0.4263 target = 0.094220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.087774 restraints weight = 21073.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.089918 restraints weight = 7363.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.091217 restraints weight = 3454.017| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.7284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2076 Z= 0.080 Angle : 0.415 4.290 2820 Z= 0.229 Chirality : 0.045 0.119 324 Planarity : 0.001 0.004 372 Dihedral : 8.009 40.471 300 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 1.39 % Allowed : 30.09 % Favored : 68.52 % 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: -5.56 (0.31), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.24), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS K 18 PHE 0.009 0.001 PHE F 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2241.16 seconds wall clock time: 40 minutes 53.72 seconds (2453.72 seconds total)