Starting phenix.real_space_refine on Fri Aug 22 16:48:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9opv_70725/08_2025/9opv_70725.cif Found real_map, /net/cci-nas-00/data/ceres_data/9opv_70725/08_2025/9opv_70725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9opv_70725/08_2025/9opv_70725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9opv_70725/08_2025/9opv_70725.map" model { file = "/net/cci-nas-00/data/ceres_data/9opv_70725/08_2025/9opv_70725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9opv_70725/08_2025/9opv_70725.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.042 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 S 5 5.16 5 C 3740 2.51 5 N 1205 2.21 5 O 1195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6145 Number of models: 1 Model: "" Number of chains: 10 Chain: "M" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 603 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 2 Chain: "N" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 626 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 603 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 2 Chain: "P" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 626 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Chain: "Q" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 603 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 2 Chain: "R" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 626 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Chain: "S" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 603 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 2 Chain: "T" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 626 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Chain: "U" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 603 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 2 Chain: "V" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 626 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Time building chain proxies: 1.81, per 1000 atoms: 0.29 Number of scatterers: 6145 At special positions: 0 Unit cell: (115.5, 117.7, 110, 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) S 5 16.00 O 1195 8.00 N 1205 7.00 C 3740 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: 0.39 Conformation dependent library (CDL) restraints added in 148.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 96.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'M' and resid 33 through 44 removed outlier: 3.700A pdb=" N MET M 44 " --> pdb=" O LEU M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 62 Processing helix chain 'M' and resid 104 through 154 removed outlier: 4.363A pdb=" N THR M 154 " --> pdb=" O LEU M 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 65 Processing helix chain 'N' and resid 106 through 169 removed outlier: 3.611A pdb=" N ASN N 123 " --> pdb=" O GLU N 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 44 removed outlier: 3.728A pdb=" N MET O 44 " --> pdb=" O LEU O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 62 Processing helix chain 'O' and resid 104 through 154 removed outlier: 3.824A pdb=" N THR O 154 " --> pdb=" O LEU O 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 65 Processing helix chain 'P' and resid 106 through 169 Processing helix chain 'Q' and resid 34 through 44 removed outlier: 3.781A pdb=" N MET Q 44 " --> pdb=" O LEU Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 62 Processing helix chain 'Q' and resid 104 through 154 Processing helix chain 'R' and resid 51 through 65 Processing helix chain 'R' and resid 106 through 169 removed outlier: 3.909A pdb=" N ASN R 123 " --> pdb=" O GLU R 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN R 124 " --> pdb=" O GLY R 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 44 removed outlier: 3.776A pdb=" N MET S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 62 Processing helix chain 'S' and resid 104 through 154 Processing helix chain 'T' and resid 51 through 65 Processing helix chain 'T' and resid 106 through 169 Processing helix chain 'U' and resid 34 through 44 removed outlier: 3.546A pdb=" N MET U 44 " --> pdb=" O LEU U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 62 Processing helix chain 'U' and resid 104 through 154 Processing helix chain 'V' and resid 51 through 65 Processing helix chain 'V' and resid 106 through 169 646 hydrogen bonds defined for protein. 1938 hydrogen bond angles 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: 0.97 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1991 1.34 - 1.45: 640 1.45 - 1.57: 3519 1.57 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 6160 Sorted by residual: bond pdb=" C VAL O 117 " pdb=" O VAL O 117 " ideal model delta sigma weight residual 1.237 1.247 -0.010 1.13e-02 7.83e+03 7.38e-01 bond pdb=" N GLN P 144 " pdb=" CA GLN P 144 " ideal model delta sigma weight residual 1.459 1.469 -0.011 1.28e-02 6.10e+03 6.83e-01 bond pdb=" C LEU P 143 " pdb=" N GLN P 144 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.38e-02 5.25e+03 6.26e-01 bond pdb=" C GLY N 120 " pdb=" O GLY N 120 " ideal model delta sigma weight residual 1.234 1.243 -0.009 1.19e-02 7.06e+03 5.98e-01 bond pdb=" CG1 ILE Q 122 " pdb=" CD1 ILE Q 122 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 5.73e-01 ... (remaining 6155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 8136 1.68 - 3.35: 123 3.35 - 5.03: 15 5.03 - 6.71: 9 6.71 - 8.39: 2 Bond angle restraints: 8285 Sorted by residual: angle pdb=" C LEU P 143 " pdb=" N GLN P 144 " pdb=" CA GLN P 144 " ideal model delta sigma weight residual 120.31 114.61 5.70 1.52e+00 4.33e-01 1.41e+01 angle pdb=" N GLN P 144 " pdb=" CA GLN P 144 " pdb=" CB GLN P 144 " ideal model delta sigma weight residual 110.28 115.90 -5.62 1.55e+00 4.16e-01 1.32e+01 angle pdb=" C GLY O 120 " pdb=" N TYR O 121 " pdb=" CA TYR O 121 " ideal model delta sigma weight residual 121.58 114.79 6.79 1.95e+00 2.63e-01 1.21e+01 angle pdb=" N GLU T 159 " pdb=" CA GLU T 159 " pdb=" CB GLU T 159 " ideal model delta sigma weight residual 110.28 114.73 -4.45 1.55e+00 4.16e-01 8.26e+00 angle pdb=" N GLN O 144 " pdb=" CA GLN O 144 " pdb=" CB GLN O 144 " ideal model delta sigma weight residual 110.12 114.32 -4.20 1.47e+00 4.63e-01 8.18e+00 ... (remaining 8280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.56: 3216 15.56 - 31.12: 444 31.12 - 46.69: 85 46.69 - 62.25: 20 62.25 - 77.81: 10 Dihedral angle restraints: 3775 sinusoidal: 1550 harmonic: 2225 Sorted by residual: dihedral pdb=" CG ARG S 152 " pdb=" CD ARG S 152 " pdb=" NE ARG S 152 " pdb=" CZ ARG S 152 " ideal model delta sinusoidal sigma weight residual 180.00 136.01 43.99 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG O 152 " pdb=" CD ARG O 152 " pdb=" NE ARG O 152 " pdb=" CZ ARG O 152 " ideal model delta sinusoidal sigma weight residual -90.00 -133.65 43.65 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CA ASP U 52 " pdb=" CB ASP U 52 " pdb=" CG ASP U 52 " pdb=" OD1 ASP U 52 " ideal model delta sinusoidal sigma weight residual -30.00 -84.65 54.65 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 3772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 704 0.031 - 0.062: 176 0.062 - 0.092: 83 0.092 - 0.123: 11 0.123 - 0.154: 1 Chirality restraints: 975 Sorted by residual: chirality pdb=" CA TYR O 121 " pdb=" N TYR O 121 " pdb=" C TYR O 121 " pdb=" CB TYR O 121 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CG LEU Q 132 " pdb=" CB LEU Q 132 " pdb=" CD1 LEU Q 132 " pdb=" CD2 LEU Q 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.48 -0.11 2.00e-01 2.50e+01 3.13e-01 chirality pdb=" CA GLN P 144 " pdb=" N GLN P 144 " pdb=" C GLN P 144 " pdb=" CB GLN P 144 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.83e-01 ... (remaining 972 not shown) Planarity restraints: 1115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE O 126 " -0.010 2.00e-02 2.50e+03 1.02e-02 1.80e+00 pdb=" CG PHE O 126 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE O 126 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE O 126 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE O 126 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE O 126 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE O 126 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 152 " -0.093 9.50e-02 1.11e+02 4.19e-02 1.35e+00 pdb=" NE ARG P 152 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG P 152 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG P 152 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG P 152 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR O 121 " -0.006 2.00e-02 2.50e+03 1.11e-02 1.23e+00 pdb=" C TYR O 121 " 0.019 2.00e-02 2.50e+03 pdb=" O TYR O 121 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE O 122 " -0.007 2.00e-02 2.50e+03 ... (remaining 1112 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2188 2.89 - 3.39: 7414 3.39 - 3.89: 10029 3.89 - 4.40: 10210 4.40 - 4.90: 16321 Nonbonded interactions: 46162 Sorted by model distance: nonbonded pdb=" O ALA P 140 " pdb=" OE1 GLN P 144 " model vdw 2.387 3.040 nonbonded pdb=" O ALA T 155 " pdb=" OE1 GLU T 159 " model vdw 2.458 3.040 nonbonded pdb=" O GLU Q 130 " pdb=" OE1 GLU Q 134 " model vdw 2.490 3.040 nonbonded pdb=" O ALA O 140 " pdb=" OE1 GLN O 144 " model vdw 2.511 3.040 nonbonded pdb=" O ALA R 140 " pdb=" OE1 GLN R 144 " model vdw 2.518 3.040 ... (remaining 46157 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 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.440 Find NCS groups from input model: 0.100 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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 : 0.002 0.030 6160 Z= 0.142 Angle : 0.528 8.387 8285 Z= 0.289 Chirality : 0.034 0.154 975 Planarity : 0.003 0.042 1115 Dihedral : 14.949 77.809 2325 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.08 (0.27), residues: 730 helix: 4.05 (0.17), residues: 695 sheet: None (None), residues: 0 loop : 0.83 (0.64), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 152 TYR 0.018 0.002 TYR M 60 PHE 0.023 0.001 PHE O 126 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 6160) covalent geometry : angle 0.52823 ( 8285) hydrogen bonds : bond 0.07448 ( 646) hydrogen bonds : angle 3.64545 ( 1938) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 55 ASP cc_start: 0.8377 (t0) cc_final: 0.7925 (m-30) REVERT: P 56 THR cc_start: 0.9533 (m) cc_final: 0.9304 (p) REVERT: Q 56 THR cc_start: 0.6769 (m) cc_final: 0.4604 (p) REVERT: R 118 LEU cc_start: 0.7504 (tt) cc_final: 0.7220 (mt) REVERT: V 149 GLU cc_start: 0.7271 (pt0) cc_final: 0.6982 (pt0) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.1397 time to fit residues: 46.0776 Evaluate side-chains 140 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 chunk 74 optimal weight: 10.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 ASN ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 ASN V 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.069003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.065012 restraints weight = 58187.567| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 4.53 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6160 Z= 0.197 Angle : 0.734 11.593 8285 Z= 0.387 Chirality : 0.038 0.149 975 Planarity : 0.005 0.031 1115 Dihedral : 3.299 15.054 880 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.24 % Allowed : 19.84 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.87 (0.26), residues: 730 helix: 3.25 (0.16), residues: 700 sheet: None (None), residues: 0 loop : 0.94 (0.96), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 163 TYR 0.032 0.002 TYR M 60 PHE 0.033 0.002 PHE U 126 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6160) covalent geometry : angle 0.73419 ( 8285) hydrogen bonds : bond 0.06876 ( 646) hydrogen bonds : angle 4.20068 ( 1938) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 143 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8790 (tp) REVERT: P 56 THR cc_start: 0.9613 (m) cc_final: 0.9357 (p) REVERT: R 118 LEU cc_start: 0.7769 (tt) cc_final: 0.7281 (mt) REVERT: R 150 LEU cc_start: 0.8485 (pp) cc_final: 0.7856 (tp) REVERT: S 143 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9060 (tp) REVERT: T 121 TYR cc_start: 0.6076 (OUTLIER) cc_final: 0.4453 (t80) outliers start: 33 outliers final: 23 residues processed: 190 average time/residue: 0.0940 time to fit residues: 22.0488 Evaluate side-chains 150 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain P residue 54 ASN Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 144 GLN Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 112 ASN Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Chi-restraints excluded: chain V residue 146 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 54 ASN ** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 ASN R 54 ASN R 144 GLN ** U 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.067847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.063811 restraints weight = 57620.543| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 4.50 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6160 Z= 0.168 Angle : 0.687 8.835 8285 Z= 0.365 Chirality : 0.036 0.173 975 Planarity : 0.004 0.031 1115 Dihedral : 3.229 13.431 880 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.44 % Allowed : 24.13 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.99 (0.26), residues: 730 helix: 3.34 (0.17), residues: 695 sheet: None (None), residues: 0 loop : 0.96 (0.96), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 133 TYR 0.027 0.002 TYR M 60 PHE 0.039 0.002 PHE M 126 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6160) covalent geometry : angle 0.68702 ( 8285) hydrogen bonds : bond 0.06819 ( 646) hydrogen bonds : angle 3.98922 ( 1938) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 52 ASP cc_start: 0.6935 (p0) cc_final: 0.6270 (m-30) REVERT: P 56 THR cc_start: 0.9598 (m) cc_final: 0.9368 (p) REVERT: P 121 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.6147 (t80) REVERT: R 118 LEU cc_start: 0.7783 (tt) cc_final: 0.7331 (mt) REVERT: S 143 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9094 (tp) REVERT: T 121 TYR cc_start: 0.6105 (OUTLIER) cc_final: 0.4563 (t80) REVERT: V 146 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7725 (mmt-90) outliers start: 28 outliers final: 16 residues processed: 166 average time/residue: 0.1010 time to fit residues: 20.8588 Evaluate side-chains 150 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Chi-restraints excluded: chain V residue 146 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 47 optimal weight: 30.0000 chunk 31 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 142 GLN ** 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 = 0.3926 r_free = 0.3926 target = 0.066751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.062986 restraints weight = 59053.051| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 4.44 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6160 Z= 0.180 Angle : 0.671 10.554 8285 Z= 0.363 Chirality : 0.037 0.210 975 Planarity : 0.004 0.022 1115 Dihedral : 3.333 14.285 880 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.24 % Allowed : 25.71 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.63 (0.27), residues: 730 helix: 3.09 (0.17), residues: 700 sheet: None (None), residues: 0 loop : 1.14 (1.07), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG T 160 TYR 0.019 0.002 TYR M 60 PHE 0.028 0.002 PHE M 126 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6160) covalent geometry : angle 0.67132 ( 8285) hydrogen bonds : bond 0.07133 ( 646) hydrogen bonds : angle 4.17772 ( 1938) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 52 ASP cc_start: 0.7035 (p0) cc_final: 0.6501 (m-30) REVERT: O 121 TYR cc_start: 0.6926 (t80) cc_final: 0.6603 (t80) REVERT: O 143 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8912 (tp) REVERT: P 56 THR cc_start: 0.9630 (m) cc_final: 0.9371 (p) REVERT: P 121 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.6216 (t80) REVERT: R 118 LEU cc_start: 0.7793 (tt) cc_final: 0.7294 (mt) REVERT: S 143 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9073 (tp) REVERT: T 113 ASN cc_start: 0.8340 (m110) cc_final: 0.6912 (m110) REVERT: T 121 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.4672 (t80) outliers start: 33 outliers final: 23 residues processed: 167 average time/residue: 0.0958 time to fit residues: 19.7814 Evaluate side-chains 150 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 ASN Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 112 ASN Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Chi-restraints excluded: chain V residue 146 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.067445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.063578 restraints weight = 60087.579| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 4.60 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6160 Z= 0.167 Angle : 0.692 12.563 8285 Z= 0.363 Chirality : 0.036 0.141 975 Planarity : 0.004 0.029 1115 Dihedral : 3.288 14.057 880 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.92 % Allowed : 28.41 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.71 (0.27), residues: 730 helix: 3.20 (0.17), residues: 695 sheet: None (None), residues: 0 loop : 0.07 (1.07), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 160 TYR 0.035 0.002 TYR U 60 PHE 0.023 0.001 PHE M 126 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6160) covalent geometry : angle 0.69219 ( 8285) hydrogen bonds : bond 0.07040 ( 646) hydrogen bonds : angle 4.06001 ( 1938) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 52 ASP cc_start: 0.7022 (p0) cc_final: 0.6661 (m-30) REVERT: O 121 TYR cc_start: 0.6955 (t80) cc_final: 0.6572 (t80) REVERT: O 143 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8996 (tp) REVERT: P 56 THR cc_start: 0.9575 (m) cc_final: 0.9316 (p) REVERT: P 121 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.6500 (t80) REVERT: R 118 LEU cc_start: 0.7815 (tt) cc_final: 0.7271 (mt) REVERT: R 150 LEU cc_start: 0.8221 (pp) cc_final: 0.7978 (tp) REVERT: S 121 TYR cc_start: 0.7037 (t80) cc_final: 0.6692 (t80) REVERT: S 143 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9111 (tp) REVERT: T 121 TYR cc_start: 0.6192 (OUTLIER) cc_final: 0.4714 (t80) REVERT: V 52 ASP cc_start: 0.7183 (p0) cc_final: 0.6826 (p0) outliers start: 31 outliers final: 23 residues processed: 164 average time/residue: 0.0991 time to fit residues: 19.9776 Evaluate side-chains 148 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 ASN Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 51 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.067565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.063772 restraints weight = 59922.979| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 4.51 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6160 Z= 0.161 Angle : 0.683 11.461 8285 Z= 0.362 Chirality : 0.035 0.131 975 Planarity : 0.003 0.030 1115 Dihedral : 3.228 13.789 880 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 5.71 % Allowed : 27.46 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.85 (0.27), residues: 730 helix: 3.30 (0.17), residues: 695 sheet: None (None), residues: 0 loop : -0.23 (1.03), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 163 TYR 0.021 0.002 TYR U 60 PHE 0.019 0.001 PHE M 126 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6160) covalent geometry : angle 0.68253 ( 8285) hydrogen bonds : bond 0.06859 ( 646) hydrogen bonds : angle 3.99362 ( 1938) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 52 ASP cc_start: 0.7000 (p0) cc_final: 0.6685 (m-30) REVERT: N 166 ASP cc_start: 0.7883 (t0) cc_final: 0.7615 (t0) REVERT: O 121 TYR cc_start: 0.6763 (t80) cc_final: 0.6386 (t80) REVERT: O 143 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8885 (tp) REVERT: P 56 THR cc_start: 0.9591 (m) cc_final: 0.9344 (p) REVERT: P 121 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.6661 (t80) REVERT: R 118 LEU cc_start: 0.7792 (tt) cc_final: 0.7240 (mt) REVERT: S 121 TYR cc_start: 0.7025 (t80) cc_final: 0.6780 (t80) REVERT: T 121 TYR cc_start: 0.6027 (OUTLIER) cc_final: 0.4661 (t80) REVERT: V 52 ASP cc_start: 0.6958 (p0) cc_final: 0.6624 (p0) outliers start: 36 outliers final: 25 residues processed: 157 average time/residue: 0.1013 time to fit residues: 19.5496 Evaluate side-chains 149 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 ASN Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.067559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.063649 restraints weight = 57913.713| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 4.45 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.6365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6160 Z= 0.171 Angle : 0.697 10.208 8285 Z= 0.374 Chirality : 0.036 0.134 975 Planarity : 0.004 0.028 1115 Dihedral : 3.338 15.148 880 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.56 % Allowed : 29.52 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.65 (0.27), residues: 730 helix: 3.11 (0.17), residues: 700 sheet: None (None), residues: 0 loop : 0.96 (1.08), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 163 TYR 0.015 0.002 TYR S 121 PHE 0.017 0.001 PHE M 126 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6160) covalent geometry : angle 0.69674 ( 8285) hydrogen bonds : bond 0.07026 ( 646) hydrogen bonds : angle 4.09678 ( 1938) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 52 ASP cc_start: 0.6918 (p0) cc_final: 0.6644 (m-30) REVERT: O 121 TYR cc_start: 0.6659 (t80) cc_final: 0.6271 (t80) REVERT: O 143 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8886 (tp) REVERT: P 56 THR cc_start: 0.9569 (m) cc_final: 0.9320 (p) REVERT: P 121 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.6692 (t80) REVERT: Q 44 MET cc_start: 0.6329 (pmm) cc_final: 0.5481 (pmm) REVERT: R 118 LEU cc_start: 0.7707 (tt) cc_final: 0.7216 (mt) REVERT: S 121 TYR cc_start: 0.7016 (t80) cc_final: 0.6711 (t80) REVERT: S 143 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9014 (tp) REVERT: T 121 TYR cc_start: 0.6090 (OUTLIER) cc_final: 0.4602 (t80) REVERT: V 52 ASP cc_start: 0.7014 (p0) cc_final: 0.6705 (p0) outliers start: 35 outliers final: 26 residues processed: 154 average time/residue: 0.0867 time to fit residues: 16.6702 Evaluate side-chains 154 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 ASN Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 119 GLU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 144 GLN ** 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 = 0.3949 r_free = 0.3949 target = 0.067548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.063546 restraints weight = 57809.011| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 4.57 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.6463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6160 Z= 0.169 Angle : 0.705 10.394 8285 Z= 0.380 Chirality : 0.037 0.150 975 Planarity : 0.004 0.028 1115 Dihedral : 3.357 15.353 880 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 5.40 % Allowed : 29.37 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.59 (0.27), residues: 730 helix: 3.07 (0.17), residues: 700 sheet: None (None), residues: 0 loop : 0.84 (1.08), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 163 TYR 0.020 0.002 TYR U 60 PHE 0.016 0.001 PHE M 126 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 6160) covalent geometry : angle 0.70536 ( 8285) hydrogen bonds : bond 0.06967 ( 646) hydrogen bonds : angle 4.09012 ( 1938) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 52 ASP cc_start: 0.6955 (p0) cc_final: 0.6631 (m-30) REVERT: O 121 TYR cc_start: 0.6568 (t80) cc_final: 0.6144 (t80) REVERT: O 143 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8828 (tp) REVERT: P 56 THR cc_start: 0.9578 (m) cc_final: 0.9334 (p) REVERT: P 121 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.6686 (t80) REVERT: Q 44 MET cc_start: 0.6275 (pmm) cc_final: 0.5438 (pmm) REVERT: R 118 LEU cc_start: 0.7689 (tt) cc_final: 0.7181 (mt) REVERT: S 121 TYR cc_start: 0.6958 (t80) cc_final: 0.6688 (t80) REVERT: T 121 TYR cc_start: 0.6024 (OUTLIER) cc_final: 0.4553 (t80) REVERT: V 52 ASP cc_start: 0.7085 (p0) cc_final: 0.6797 (p0) outliers start: 34 outliers final: 25 residues processed: 155 average time/residue: 0.0859 time to fit residues: 16.8431 Evaluate side-chains 153 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 ASN Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 112 ASN Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 7 optimal weight: 0.0040 chunk 55 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 overall best weight: 4.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 144 GLN ** 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 = 0.3952 r_free = 0.3952 target = 0.067760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.063933 restraints weight = 59904.914| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 4.56 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.6458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6160 Z= 0.160 Angle : 0.754 15.128 8285 Z= 0.390 Chirality : 0.036 0.141 975 Planarity : 0.004 0.038 1115 Dihedral : 3.306 15.614 880 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 4.29 % Allowed : 30.63 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.81 (0.28), residues: 730 helix: 3.22 (0.17), residues: 700 sheet: None (None), residues: 0 loop : 0.70 (1.06), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 163 TYR 0.018 0.002 TYR S 121 PHE 0.015 0.001 PHE M 126 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6160) covalent geometry : angle 0.75402 ( 8285) hydrogen bonds : bond 0.06608 ( 646) hydrogen bonds : angle 3.96743 ( 1938) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 56 THR cc_start: 0.9568 (m) cc_final: 0.9309 (p) REVERT: P 121 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.6814 (t80) REVERT: Q 44 MET cc_start: 0.6015 (pmm) cc_final: 0.5346 (pmm) REVERT: Q 134 GLU cc_start: 0.8398 (pt0) cc_final: 0.8136 (pm20) REVERT: R 118 LEU cc_start: 0.7648 (tt) cc_final: 0.7143 (mt) REVERT: T 121 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.4703 (t80) REVERT: V 52 ASP cc_start: 0.7054 (p0) cc_final: 0.6778 (p0) outliers start: 27 outliers final: 24 residues processed: 155 average time/residue: 0.0830 time to fit residues: 16.3170 Evaluate side-chains 148 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 ASN Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 112 ASN Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 56 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 ASN ** R 144 GLN ** 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 = 0.3948 r_free = 0.3948 target = 0.067624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.063654 restraints weight = 57744.135| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 4.56 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.6680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6160 Z= 0.177 Angle : 0.774 13.547 8285 Z= 0.412 Chirality : 0.038 0.174 975 Planarity : 0.004 0.041 1115 Dihedral : 3.392 15.240 880 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 4.13 % Allowed : 31.75 % Favored : 64.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.35 (0.28), residues: 730 helix: 2.96 (0.17), residues: 695 sheet: None (None), residues: 0 loop : 0.20 (0.94), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 160 TYR 0.023 0.002 TYR S 121 PHE 0.015 0.001 PHE M 126 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6160) covalent geometry : angle 0.77354 ( 8285) hydrogen bonds : bond 0.06957 ( 646) hydrogen bonds : angle 4.16196 ( 1938) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 143 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8946 (tp) REVERT: P 56 THR cc_start: 0.9542 (m) cc_final: 0.9311 (p) REVERT: P 121 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.6711 (t80) REVERT: Q 44 MET cc_start: 0.6128 (pmm) cc_final: 0.5503 (pmm) REVERT: Q 134 GLU cc_start: 0.8353 (pt0) cc_final: 0.8107 (pm20) REVERT: R 118 LEU cc_start: 0.7821 (tt) cc_final: 0.7208 (mt) REVERT: T 121 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.4625 (t80) REVERT: V 52 ASP cc_start: 0.7211 (p0) cc_final: 0.6946 (p0) outliers start: 26 outliers final: 22 residues processed: 146 average time/residue: 0.0825 time to fit residues: 15.3591 Evaluate side-chains 145 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 ASN Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 112 ASN Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 6 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** 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 = 0.3950 r_free = 0.3950 target = 0.067779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.063931 restraints weight = 58758.710| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 4.55 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6160 Z= 0.168 Angle : 0.788 13.363 8285 Z= 0.411 Chirality : 0.037 0.163 975 Planarity : 0.004 0.030 1115 Dihedral : 3.327 15.136 880 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 4.44 % Allowed : 31.59 % Favored : 63.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.46 (0.28), residues: 730 helix: 3.04 (0.18), residues: 695 sheet: None (None), residues: 0 loop : -0.01 (0.89), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 163 TYR 0.017 0.001 TYR U 60 PHE 0.015 0.001 PHE M 126 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6160) covalent geometry : angle 0.78800 ( 8285) hydrogen bonds : bond 0.06833 ( 646) hydrogen bonds : angle 4.07479 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1285.63 seconds wall clock time: 22 minutes 45.41 seconds (1365.41 seconds total)