Starting phenix.real_space_refine on Mon Sep 23 11:31:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iks_35520/09_2024/8iks_35520.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iks_35520/09_2024/8iks_35520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iks_35520/09_2024/8iks_35520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iks_35520/09_2024/8iks_35520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iks_35520/09_2024/8iks_35520.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iks_35520/09_2024/8iks_35520.cif" } resolution = 3.75 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= 0.002 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 I 32 10.91 5 C 608 2.51 5 N 176 2.21 5 O 208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 1024 Number of models: 1 Model: "" Number of chains: 16 Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "N" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "O" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "I" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'PHI:plan-2': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 0.80, per 1000 atoms: 0.78 Number of scatterers: 1024 At special positions: 0 Unit cell: (122.01, 82.17, 24.9, 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) I 32 52.95 O 208 8.00 N 176 7.00 C 608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 66.6 milliseconds 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 160 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: 0.27 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: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 487 1.39 - 1.57: 521 1.57 - 1.74: 0 1.74 - 1.92: 0 1.92 - 2.09: 32 Bond restraints: 1040 Sorted by residual: bond pdb=" CZ PHI E 222 " pdb=" I PHI E 222 " ideal model delta sigma weight residual 2.106 2.003 0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" CZ PHI L 216 " pdb=" I PHI L 216 " ideal model delta sigma weight residual 2.106 2.003 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" CZ PHI D 222 " pdb=" I PHI D 222 " ideal model delta sigma weight residual 2.106 2.003 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" CZ PHI N 222 " pdb=" I PHI N 222 " ideal model delta sigma weight residual 2.106 2.005 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" CZ PHI G 216 " pdb=" I PHI G 216 " ideal model delta sigma weight residual 2.106 2.006 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 1035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.16: 1327 8.16 - 16.32: 27 16.32 - 24.48: 11 24.48 - 32.64: 8 32.64 - 40.79: 3 Bond angle restraints: 1376 Sorted by residual: angle pdb=" C PHI M 216 " pdb=" CA PHI M 216 " pdb=" CB PHI M 216 " ideal model delta sigma weight residual 110.10 74.92 35.18 1.90e+00 2.77e-01 3.43e+02 angle pdb=" N ASP P 220 " pdb=" CA ASP P 220 " pdb=" C ASP P 220 " ideal model delta sigma weight residual 108.34 82.51 25.83 1.64e+00 3.72e-01 2.48e+02 angle pdb=" N ASP H 220 " pdb=" CA ASP H 220 " pdb=" C ASP H 220 " ideal model delta sigma weight residual 109.96 85.83 24.13 1.68e+00 3.54e-01 2.06e+02 angle pdb=" N GLY M 217 " pdb=" CA GLY M 217 " pdb=" C GLY M 217 " ideal model delta sigma weight residual 113.30 72.51 40.79 2.90e+00 1.19e-01 1.98e+02 angle pdb=" N ASN P 221 " pdb=" CA ASN P 221 " pdb=" C ASN P 221 " ideal model delta sigma weight residual 111.00 71.68 39.32 2.80e+00 1.28e-01 1.97e+02 ... (remaining 1371 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 15.47: 361 15.47 - 30.92: 34 30.92 - 46.36: 9 46.36 - 61.81: 6 61.81 - 77.25: 6 Dihedral angle restraints: 416 sinusoidal: 128 harmonic: 288 Sorted by residual: dihedral pdb=" C PHI M 222 " pdb=" N PHI M 222 " pdb=" CA PHI M 222 " pdb=" CB PHI M 222 " ideal model delta harmonic sigma weight residual -122.60 -151.95 29.35 0 2.50e+00 1.60e-01 1.38e+02 dihedral pdb=" C PHI M 216 " pdb=" N PHI M 216 " pdb=" CA PHI M 216 " pdb=" CB PHI M 216 " ideal model delta harmonic sigma weight residual -122.60 -95.34 -27.26 0 2.50e+00 1.60e-01 1.19e+02 dihedral pdb=" N PHI M 222 " pdb=" C PHI M 222 " pdb=" CA PHI M 222 " pdb=" CB PHI M 222 " ideal model delta harmonic sigma weight residual 122.80 149.14 -26.34 0 2.50e+00 1.60e-01 1.11e+02 ... (remaining 413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.250: 72 0.250 - 0.500: 2 0.500 - 0.749: 4 0.749 - 0.999: 1 0.999 - 1.249: 1 Chirality restraints: 80 Sorted by residual: chirality pdb=" CA PHI M 222 " pdb=" N PHI M 222 " pdb=" C PHI M 222 " pdb=" CB PHI M 222 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.90e+01 chirality pdb=" CA ASN F 219 " pdb=" N ASN F 219 " pdb=" C ASN F 219 " pdb=" CB ASN F 219 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" CA PHI M 216 " pdb=" N PHI M 216 " pdb=" C PHI M 216 " pdb=" CB PHI M 216 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 77 not shown) Planarity restraints: 208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 217 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C GLY F 217 " 0.033 2.00e-02 2.50e+03 pdb=" O GLY F 217 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY F 218 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN M 221 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" CG ASN M 221 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN M 221 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN M 221 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 220 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.01e+00 pdb=" CG ASP D 220 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP D 220 " 0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP D 220 " 0.006 2.00e-02 2.50e+03 ... (remaining 205 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.50: 33 2.50 - 3.11: 856 3.11 - 3.73: 1131 3.73 - 4.34: 1642 4.34 - 4.96: 2074 Nonbonded interactions: 5736 Sorted by model distance: nonbonded pdb=" O PHI M 216 " pdb=" CB PHI M 216 " model vdw 1.885 2.752 nonbonded pdb=" N GLY M 217 " pdb=" O GLY M 217 " model vdw 1.952 2.496 nonbonded pdb=" N ASN P 221 " pdb=" O ASN P 221 " model vdw 1.982 2.496 nonbonded pdb=" O ASN H 221 " pdb=" OD1 ASN H 221 " model vdw 2.002 3.040 nonbonded pdb=" O GLY M 223 " pdb=" N GLY H 215 " model vdw 2.226 3.120 ... (remaining 5731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 2.980 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.680 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4762 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 : 0.018 0.103 1040 Z= 0.906 Angle : 4.073 40.794 1376 Z= 1.888 Chirality : 0.239 1.249 80 Planarity : 0.004 0.019 208 Dihedral : 18.129 77.253 256 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 50.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 10.00 % 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: -5.59 (0.43), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.25 (0.33), residues: 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.082 Fit side-chains REVERT: F 220 ASP cc_start: 0.7737 (m-30) cc_final: 0.6743 (p0) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0660 time to fit residues: 0.7788 Evaluate side-chains 1 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 ASN ** N 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5365 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 0.144 1040 Z= 1.707 Angle : 2.984 26.954 1376 Z= 1.300 Chirality : 0.156 0.403 80 Planarity : 0.011 0.047 208 Dihedral : 25.817 88.091 160 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 82.99 Ramachandran Plot: Outliers : 4.17 % Allowed : 33.33 % Favored : 62.50 % Rotamer: Outliers : 10.42 % Allowed : 25.00 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.12 % 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: -6.20 (0.44), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.72 (0.33), residues: 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 0 time to evaluate : 0.081 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 5 average time/residue: 0.0600 time to fit residues: 0.4513 Evaluate side-chains 4 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 0 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain L residue 220 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 221 ASN ** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 221 ASN ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5370 moved from start: 0.7623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 0.144 1040 Z= 1.659 Angle : 2.956 21.758 1376 Z= 1.268 Chirality : 0.152 0.342 80 Planarity : 0.010 0.032 208 Dihedral : 25.450 86.274 160 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 80.64 Ramachandran Plot: Outliers : 2.08 % Allowed : 47.92 % Favored : 50.00 % Rotamer: Outliers : 14.58 % Allowed : 33.33 % Favored : 52.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.34 % 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: -6.91 (0.30), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.26 (0.23), residues: 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 0 time to evaluate : 0.091 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 7 average time/residue: 0.0655 time to fit residues: 0.6388 Evaluate side-chains 6 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 0 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain L residue 220 ASP Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain I residue 220 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 221 ASN D 219 ASN O 219 ASN ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5402 moved from start: 0.8264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 0.143 1040 Z= 1.647 Angle : 2.916 18.078 1376 Z= 1.256 Chirality : 0.150 0.333 80 Planarity : 0.010 0.032 208 Dihedral : 25.439 86.872 160 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 80.00 Ramachandran Plot: Outliers : 2.08 % Allowed : 50.00 % Favored : 47.92 % Rotamer: Outliers : 27.08 % Allowed : 18.75 % Favored : 54.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.91 % 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: -7.06 (0.24), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.38 (0.18), residues: 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 0 time to evaluate : 0.083 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 13 average time/residue: 0.0625 time to fit residues: 1.0478 Evaluate side-chains 8 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 0 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain L residue 220 ASP Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain I residue 220 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5363 moved from start: 0.8650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 0.143 1040 Z= 1.639 Angle : 2.955 18.691 1376 Z= 1.272 Chirality : 0.151 0.322 80 Planarity : 0.010 0.038 208 Dihedral : 25.526 86.751 160 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 75.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 52.08 % Favored : 47.92 % Rotamer: Outliers : 16.67 % Allowed : 27.08 % Favored : 56.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.91 % 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: -6.96 (0.24), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.30 (0.18), residues: 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 0 time to evaluate : 0.082 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 8 average time/residue: 0.0614 time to fit residues: 0.6667 Evaluate side-chains 7 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 0 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain L residue 220 ASP Chi-restraints excluded: chain N residue 220 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 219 ASN ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5362 moved from start: 0.8718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 0.142 1040 Z= 1.641 Angle : 2.970 18.182 1376 Z= 1.281 Chirality : 0.150 0.331 80 Planarity : 0.010 0.034 208 Dihedral : 25.735 87.001 160 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 77.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 52.08 % Favored : 47.92 % Rotamer: Outliers : 20.83 % Allowed : 25.00 % Favored : 54.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.12 % 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: -6.99 (0.24), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.32 (0.18), residues: 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 0 time to evaluate : 0.091 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 10 average time/residue: 0.0605 time to fit residues: 0.8048 Evaluate side-chains 8 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 0 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain L residue 220 ASP Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain I residue 220 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5351 moved from start: 0.8745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 0.142 1040 Z= 1.638 Angle : 2.985 18.333 1376 Z= 1.288 Chirality : 0.151 0.326 80 Planarity : 0.010 0.033 208 Dihedral : 25.771 86.881 160 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 77.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 52.08 % Favored : 47.92 % Rotamer: Outliers : 16.67 % Allowed : 25.00 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.34 % 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: -6.94 (0.26), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.29 (0.20), residues: 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 0 time to evaluate : 0.087 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 8 average time/residue: 0.0590 time to fit residues: 0.6481 Evaluate side-chains 8 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 0 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain L residue 220 ASP Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain I residue 220 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5360 moved from start: 0.8768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 0.142 1040 Z= 1.638 Angle : 2.978 18.254 1376 Z= 1.286 Chirality : 0.151 0.327 80 Planarity : 0.010 0.033 208 Dihedral : 25.806 87.043 160 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 78.19 Ramachandran Plot: Outliers : 2.08 % Allowed : 50.00 % Favored : 47.92 % Rotamer: Outliers : 20.83 % Allowed : 20.83 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.34 % 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: -6.94 (0.26), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.28 (0.20), residues: 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 0 time to evaluate : 0.071 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 10 average time/residue: 0.0545 time to fit residues: 0.7173 Evaluate side-chains 9 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 0 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain L residue 220 ASP Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain N residue 221 ASN Chi-restraints excluded: chain I residue 220 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5358 moved from start: 0.8778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 0.142 1040 Z= 1.639 Angle : 2.976 18.299 1376 Z= 1.285 Chirality : 0.151 0.325 80 Planarity : 0.010 0.033 208 Dihedral : 25.814 86.996 160 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 78.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 52.08 % Favored : 47.92 % Rotamer: Outliers : 18.75 % Allowed : 22.92 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.34 % 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: -6.93 (0.26), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.28 (0.20), residues: 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 0 time to evaluate : 0.081 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 9 average time/residue: 0.0608 time to fit residues: 0.7297 Evaluate side-chains 9 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 0 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain L residue 220 ASP Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain N residue 221 ASN Chi-restraints excluded: chain I residue 220 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5349 moved from start: 0.8791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 0.142 1040 Z= 1.640 Angle : 2.973 18.299 1376 Z= 1.283 Chirality : 0.150 0.325 80 Planarity : 0.010 0.033 208 Dihedral : 25.829 87.020 160 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 78.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 52.08 % Favored : 47.92 % Rotamer: Outliers : 18.75 % Allowed : 22.92 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.34 % 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: -6.94 (0.26), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.28 (0.20), residues: 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 96 Ramachandran restraints generated. 48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 0 time to evaluate : 0.084 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 9 average time/residue: 0.0641 time to fit residues: 0.7693 Evaluate side-chains 9 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 0 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain M residue 220 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain L residue 220 ASP Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain N residue 221 ASN Chi-restraints excluded: chain I residue 220 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 219 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 = 0.4466 r_free = 0.4466 target = 0.120772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.111049 restraints weight = 2006.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.114514 restraints weight = 780.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.115985 restraints weight = 326.454| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5300 moved from start: 0.8797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 0.142 1040 Z= 1.640 Angle : 2.970 18.315 1376 Z= 1.281 Chirality : 0.150 0.326 80 Planarity : 0.010 0.033 208 Dihedral : 25.833 87.026 160 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 78.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Rotamer: Outliers : 18.75 % Allowed : 22.92 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.34 % 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: -6.94 (0.25), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.28 (0.19), residues: 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 317.95 seconds wall clock time: 6 minutes 25.28 seconds (385.28 seconds total)