Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 15:16:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/08_2023/6zrq_11382_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/08_2023/6zrq_11382.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/08_2023/6zrq_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_11382/08_2023/6zrq_11382_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/08_2023/6zrq_11382_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/08_2023/6zrq_11382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/08_2023/6zrq_11382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/08_2023/6zrq_11382_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrq_11382/08_2023/6zrq_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-1.21rc1-5044/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: 1.74, per 1000 atoms: 0.46 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: 3.41 Conformation dependent library (CDL) restraints added in 327.5 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: 0.41 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: 3.33 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: 1176 12.47 - 24.93: 276 24.93 - 37.40: 24 37.40 - 49.86: 24 49.86 - 62.33: 24 Dihedral angle restraints: 1524 sinusoidal: 624 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 1521 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: 1.060 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: 0.050 Extract box with map and model: 5.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.740 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.380 ------------------------------------------------------------------------------- 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 : 12.353 26.190 612 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 % 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 *********************** 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 : 0.275 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 outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1242 time to fit residues: 10.3352 Evaluate side-chains 20 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.296 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3247 ------------------------------------------------------------------------------- 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: 0.7980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.3555 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= 0.106 Angle : 0.589 5.218 2820 Z= 0.301 Chirality : 0.049 0.145 324 Planarity : 0.002 0.007 372 Dihedral : 7.329 20.636 276 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.37), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.28), residues: 240 *********************** 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 51 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 51 average time/residue: 0.1260 time to fit residues: 8.6640 Evaluate side-chains 27 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0629 time to fit residues: 0.5503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** G 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: 0.6459 moved from start: 0.4952 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= 0.118 Angle : 0.541 4.535 2820 Z= 0.287 Chirality : 0.046 0.133 324 Planarity : 0.002 0.006 372 Dihedral : 7.121 25.565 276 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 2.31 % 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: -4.78 (0.28), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.22), residues: 240 *********************** 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: 5 poor density : 18 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 22 average time/residue: 0.1127 time to fit residues: 3.8026 Evaluate side-chains 18 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 13 time to evaluate : 0.289 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0467 time to fit residues: 0.7328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** ** 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: 0.6623 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.021 2076 Z= 0.191 Angle : 0.656 6.333 2820 Z= 0.334 Chirality : 0.051 0.169 324 Planarity : 0.003 0.007 372 Dihedral : 8.093 28.718 276 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 3.24 % 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: -5.38 (0.26), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.20), residues: 240 *********************** 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 13 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 6 time to evaluate : 0.312 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 12 average time/residue: 0.1118 time to fit residues: 2.2425 Evaluate side-chains 11 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 5 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0506 time to fit residues: 0.8581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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** ** I 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: 0.6656 moved from start: 0.6280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.017 2076 Z= 0.156 Angle : 0.596 5.531 2820 Z= 0.309 Chirality : 0.050 0.159 324 Planarity : 0.002 0.006 372 Dihedral : 7.432 26.897 276 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 24.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.42 % Favored : 84.58 % Rotamer Outliers : 3.24 % 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: -5.64 (0.27), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.29 (0.20), residues: 240 *********************** 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 14 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 7 time to evaluate : 0.337 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 14 average time/residue: 0.0944 time to fit residues: 2.2505 Evaluate side-chains 11 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 5 time to evaluate : 0.288 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.0472 time to fit residues: 0.7917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 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: 0.6642 moved from start: 0.6531 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= 0.109 Angle : 0.509 4.833 2820 Z= 0.269 Chirality : 0.048 0.139 324 Planarity : 0.002 0.005 372 Dihedral : 7.029 30.305 276 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer Outliers : 1.39 % 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 (0.27), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.29 (0.21), residues: 240 *********************** 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 17 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 14 time to evaluate : 0.328 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 17 average time/residue: 0.1030 time to fit residues: 2.7818 Evaluate side-chains 13 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.335 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0563 time to fit residues: 0.4025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.6681 moved from start: 0.6826 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= 0.126 Angle : 0.524 4.600 2820 Z= 0.278 Chirality : 0.048 0.146 324 Planarity : 0.002 0.004 372 Dihedral : 7.344 28.509 276 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.33 % Favored : 81.67 % Rotamer Outliers : 1.39 % 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: -5.76 (0.27), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.21), residues: 240 *********************** 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 13 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 10 time to evaluate : 0.333 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 13 average time/residue: 0.1105 time to fit residues: 2.3778 Evaluate side-chains 13 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 10 time to evaluate : 0.330 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0612 time to fit residues: 0.6438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.6671 moved from start: 0.6993 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= 0.123 Angle : 0.502 4.555 2820 Z= 0.270 Chirality : 0.048 0.141 324 Planarity : 0.002 0.004 372 Dihedral : 7.094 26.879 276 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.50 % Favored : 82.50 % Rotamer Outliers : 2.31 % 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: -5.81 (0.27), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.42 (0.20), residues: 240 *********************** 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: 5 poor density : 12 time to evaluate : 0.353 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 16 average time/residue: 0.1202 time to fit residues: 3.1228 Evaluate side-chains 15 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 12 time to evaluate : 0.335 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0537 time to fit residues: 0.6022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.0070 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.0070 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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: 0.6643 moved from start: 0.7067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.009 2076 Z= 0.083 Angle : 0.438 3.252 2820 Z= 0.243 Chirality : 0.046 0.119 324 Planarity : 0.001 0.004 372 Dihedral : 6.819 28.812 276 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.82 (0.27), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.43 (0.21), residues: 240 *********************** 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 13 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.354 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 13 average time/residue: 0.1111 time to fit residues: 2.4449 Evaluate side-chains 13 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.332 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0632 time to fit residues: 0.4636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.0000 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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: 0.6637 moved from start: 0.7202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.010 2076 Z= 0.077 Angle : 0.418 2.743 2820 Z= 0.234 Chirality : 0.045 0.120 324 Planarity : 0.001 0.004 372 Dihedral : 6.527 25.080 276 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.82 (0.27), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.43 (0.21), residues: 240 ********************** 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: 1 poor density : 15 time to evaluate : 0.321 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.1000 time to fit residues: 2.6180 Evaluate side-chains 15 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.322 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0562 time to fit residues: 0.4415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 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 = 0.4229 r_free = 0.4229 target = 0.092315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.085757 restraints weight = 21384.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.087887 restraints weight = 7442.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.089189 restraints weight = 3550.497| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.7300 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= 0.100 Angle : 0.450 4.064 2820 Z= 0.246 Chirality : 0.046 0.120 324 Planarity : 0.001 0.004 372 Dihedral : 6.576 25.657 276 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.25 % Favored : 83.75 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.88 (0.27), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.47 (0.20), residues: 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2167.34 seconds wall clock time: 39 minutes 51.52 seconds (2391.52 seconds total)