Starting phenix.real_space_refine on Mon Feb 10 19:26:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iks_35520/02_2025/8iks_35520.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iks_35520/02_2025/8iks_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/cci-nas-00/data/ceres_data/8iks_35520/02_2025/8iks_35520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iks_35520/02_2025/8iks_35520.map" model { file = "/net/cci-nas-00/data/ceres_data/8iks_35520/02_2025/8iks_35520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iks_35520/02_2025/8iks_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-5592/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: 0.60, per 1000 atoms: 0.59 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: 0.44 Conformation dependent library (CDL) restraints added in 85.9 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: 0.36 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: 0.37 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: 2.600 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: 0.000 Set scattering table: 0.020 Process input model: 8.870 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.430 ------------------------------------------------------------------------------- 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 to be fit. 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: 0.0680 time to fit residues: 0.8018 Evaluate side-chains 1 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.083 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.103831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.097960 restraints weight = 2363.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.099986 restraints weight = 1007.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.100758 restraints weight = 469.744| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5178 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 to be fit. rotamer outliers: 5 poor density : 0 time to evaluate : 0.074 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 5 average time/residue: 0.0570 time to fit residues: 0.4244 Evaluate side-chains 4 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 0 time to evaluate : 0.061 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.118011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.110544 restraints weight = 1919.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.113128 restraints weight = 796.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.114736 restraints weight = 365.680| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5306 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 to be fit. rotamer outliers: 7 poor density : 0 time to evaluate : 0.081 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 7 average time/residue: 0.0620 time to fit residues: 0.6049 Evaluate side-chains 6 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 ASN ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.118766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.110313 restraints weight = 1881.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.113245 restraints weight = 744.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.114664 restraints weight = 323.622| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.8257 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= 1.645 Angle : 2.920 18.123 1376 Z= 1.256 Chirality : 0.150 0.328 80 Planarity : 0.010 0.033 208 Dihedral : 25.395 86.819 160 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 78.24 Ramachandran Plot: Outliers : 2.08 % Allowed : 50.00 % Favored : 47.92 % Rotamer: Outliers : 22.92 % Allowed : 20.83 % 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: -7.07 (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 11 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 0 time to evaluate : 0.065 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 11 average time/residue: 0.0512 time to fit residues: 0.7376 Evaluate side-chains 7 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 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 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: D 219 ASN ** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.120340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.111660 restraints weight = 1949.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.115181 restraints weight = 770.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.115934 restraints weight = 326.609| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5290 moved from start: 0.8701 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= 1.641 Angle : 2.954 18.634 1376 Z= 1.272 Chirality : 0.151 0.326 80 Planarity : 0.010 0.032 208 Dihedral : 25.611 86.642 160 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 76.43 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 : 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: -6.98 (0.24), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.32 (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 10 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 0 time to evaluate : 0.075 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 10 average time/residue: 0.0577 time to fit residues: 0.7590 Evaluate side-chains 8 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 0 time to evaluate : 0.073 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.121273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.111933 restraints weight = 1832.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.114664 restraints weight = 731.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.116839 restraints weight = 343.800| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5261 moved from start: 0.8726 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 : 2.977 18.098 1376 Z= 1.284 Chirality : 0.151 0.327 80 Planarity : 0.010 0.040 208 Dihedral : 25.740 86.978 160 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 78.78 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: -6.95 (0.24), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.29 (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 to be fit. rotamer outliers: 10 poor density : 0 time to evaluate : 0.079 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 10 average time/residue: 0.0586 time to fit residues: 0.7785 Evaluate side-chains 8 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 0 time to evaluate : 0.079 ------------------------------------------------------------------------------- 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: 0.9980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.120136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.111715 restraints weight = 1970.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.115160 restraints weight = 775.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.116652 restraints weight = 322.334| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5280 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 : 2.983 18.335 1376 Z= 1.287 Chirality : 0.152 0.328 80 Planarity : 0.010 0.035 208 Dihedral : 25.787 86.892 160 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 : 18.75 % Allowed : 20.83 % Favored : 60.42 % 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: -6.92 (0.26), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.27 (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 9 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 0 time to evaluate : 0.074 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 9 average time/residue: 0.0593 time to fit residues: 0.6984 Evaluate side-chains 9 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 0 time to evaluate : 0.076 ------------------------------------------------------------------------------- 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=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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.120529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.112149 restraints weight = 1938.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.115414 restraints weight = 776.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.116710 restraints weight = 321.959| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5289 moved from start: 0.8765 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 : 2.976 18.314 1376 Z= 1.284 Chirality : 0.151 0.326 80 Planarity : 0.010 0.034 208 Dihedral : 25.805 86.977 160 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 77.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 52.08 % Favored : 47.92 % Rotamer: Outliers : 20.83 % Allowed : 18.75 % Favored : 60.42 % 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: -6.92 (0.26), residues: 48 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.27 (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 to be fit. rotamer outliers: 10 poor density : 0 time to evaluate : 0.081 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 10 average time/residue: 0.0605 time to fit residues: 0.7997 Evaluate side-chains 9 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 0 time to evaluate : 0.081 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.121081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.112371 restraints weight = 1960.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.115172 restraints weight = 798.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.117062 restraints weight = 355.816| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5269 moved from start: 0.8787 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= 1.637 Angle : 2.973 18.307 1376 Z= 1.283 Chirality : 0.151 0.324 80 Planarity : 0.010 0.034 208 Dihedral : 25.809 86.981 160 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 79.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 52.08 % Favored : 47.92 % Rotamer: Outliers : 18.75 % Allowed : 20.83 % Favored : 60.42 % 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 : -5.27 (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 to be fit. 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: 0.0653 time to fit residues: 0.7833 Evaluate side-chains 9 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.121764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.112489 restraints weight = 1783.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.115718 restraints weight = 758.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.116670 restraints weight = 318.822| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5276 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 : 2.973 18.282 1376 Z= 1.283 Chirality : 0.151 0.326 80 Planarity : 0.010 0.034 208 Dihedral : 25.816 87.030 160 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 79.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 47.92 % Favored : 52.08 % Rotamer: Outliers : 18.75 % Allowed : 20.83 % Favored : 60.42 % 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 : -5.27 (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 to be fit. 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: 0.0632 time to fit residues: 0.7922 Evaluate side-chains 9 residues out of total 48 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 0 time to evaluate : 0.081 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.121270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.111964 restraints weight = 1897.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.115224 restraints weight = 812.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.117095 restraints weight = 337.010| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5273 moved from start: 0.8806 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 : 2.970 18.353 1376 Z= 1.282 Chirality : 0.151 0.325 80 Planarity : 0.010 0.034 208 Dihedral : 25.827 87.023 160 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 79.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 47.92 % Favored : 52.08 % Rotamer: Outliers : 18.75 % Allowed : 20.83 % Favored : 60.42 % 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: 388.87 seconds wall clock time: 8 minutes 5.01 seconds (485.01 seconds total)