Starting phenix.real_space_refine on Tue Feb 3 17:12:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wz6_66383/02_2026/9wz6_66383.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wz6_66383/02_2026/9wz6_66383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wz6_66383/02_2026/9wz6_66383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wz6_66383/02_2026/9wz6_66383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wz6_66383/02_2026/9wz6_66383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wz6_66383/02_2026/9wz6_66383.map" } resolution = 2.66 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= 0.004 sd= 0.019 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 56 5.16 5 C 3464 2.51 5 N 952 2.21 5 O 1072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5544 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "B" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "C" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "D" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "E" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "F" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "H" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Time building chain proxies: 1.42, per 1000 atoms: 0.26 Number of scatterers: 5544 At special positions: 0 Unit cell: (84.15, 85.85, 79.05, 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 56 16.00 O 1072 8.00 N 952 7.00 C 3464 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 309.3 milliseconds 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 92.0% 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 'A' and resid 1 through 8 Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 18 through 32 Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 49 through 62 Processing helix chain 'A' and resid 65 through 80 removed outlier: 3.718A pdb=" N CYS A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 9 through 17 Processing helix chain 'B' and resid 18 through 32 Processing helix chain 'B' and resid 36 through 46 Processing helix chain 'B' and resid 49 through 62 Processing helix chain 'B' and resid 65 through 80 removed outlier: 3.582A pdb=" N CYS B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 88 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 18 through 32 Processing helix chain 'C' and resid 36 through 46 Processing helix chain 'C' and resid 49 through 62 Processing helix chain 'C' and resid 65 through 80 removed outlier: 3.659A pdb=" N CYS C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 9 through 17 Processing helix chain 'D' and resid 18 through 32 Processing helix chain 'D' and resid 36 through 46 Processing helix chain 'D' and resid 49 through 62 Processing helix chain 'D' and resid 65 through 80 removed outlier: 3.653A pdb=" N CYS D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 71 " --> pdb=" O GLN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 88 Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 9 through 17 Processing helix chain 'E' and resid 18 through 32 Processing helix chain 'E' and resid 36 through 46 Processing helix chain 'E' and resid 49 through 62 Processing helix chain 'E' and resid 65 through 80 removed outlier: 3.641A pdb=" N ILE E 71 " --> pdb=" O GLN E 67 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS E 72 " --> pdb=" O ALA E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 88 Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 9 through 17 Processing helix chain 'F' and resid 18 through 32 Processing helix chain 'F' and resid 36 through 46 Processing helix chain 'F' and resid 49 through 62 Processing helix chain 'F' and resid 65 through 80 removed outlier: 3.657A pdb=" N ILE F 71 " --> pdb=" O GLN F 67 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS F 72 " --> pdb=" O ALA F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 88 Processing helix chain 'G' and resid 2 through 9 Processing helix chain 'G' and resid 9 through 17 Processing helix chain 'G' and resid 18 through 32 Processing helix chain 'G' and resid 36 through 46 Processing helix chain 'G' and resid 49 through 62 Processing helix chain 'G' and resid 65 through 80 removed outlier: 3.533A pdb=" N CYS G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE G 71 " --> pdb=" O GLN G 67 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'H' and resid 2 through 9 Processing helix chain 'H' and resid 9 through 17 Processing helix chain 'H' and resid 18 through 32 Processing helix chain 'H' and resid 36 through 46 Processing helix chain 'H' and resid 49 through 62 Processing helix chain 'H' and resid 65 through 80 removed outlier: 3.597A pdb=" N CYS H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE H 71 " --> pdb=" O GLN H 67 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 88 416 hydrogen bonds defined for protein. 1248 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: 0.77 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1856 1.34 - 1.46: 813 1.46 - 1.58: 2811 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 5568 Sorted by residual: bond pdb=" N ILE D 62 " pdb=" CA ILE D 62 " ideal model delta sigma weight residual 1.463 1.471 -0.008 1.20e-02 6.94e+03 4.07e-01 bond pdb=" CA ARG C 33 " pdb=" C ARG C 33 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.45e-02 4.76e+03 4.03e-01 bond pdb=" CA ARG A 33 " pdb=" C ARG A 33 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.45e-02 4.76e+03 3.96e-01 bond pdb=" CB GLU B 8 " pdb=" CG GLU B 8 " ideal model delta sigma weight residual 1.520 1.538 -0.018 3.00e-02 1.11e+03 3.51e-01 bond pdb=" CG1 ILE D 22 " pdb=" CD1 ILE D 22 " ideal model delta sigma weight residual 1.513 1.490 0.023 3.90e-02 6.57e+02 3.42e-01 ... (remaining 5563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 7077 0.92 - 1.84: 316 1.84 - 2.76: 31 2.76 - 3.68: 6 3.68 - 4.60: 10 Bond angle restraints: 7440 Sorted by residual: angle pdb=" N ALA C 2 " pdb=" CA ALA C 2 " pdb=" C ALA C 2 " ideal model delta sigma weight residual 111.28 113.89 -2.61 1.09e+00 8.42e-01 5.72e+00 angle pdb=" N GLY G 65 " pdb=" CA GLY G 65 " pdb=" C GLY G 65 " ideal model delta sigma weight residual 111.52 114.36 -2.84 1.31e+00 5.83e-01 4.72e+00 angle pdb=" N GLY H 65 " pdb=" CA GLY H 65 " pdb=" C GLY H 65 " ideal model delta sigma weight residual 111.52 114.18 -2.66 1.31e+00 5.83e-01 4.13e+00 angle pdb=" CA GLY D 88 " pdb=" C GLY D 88 " pdb=" N LEU D 89 " ideal model delta sigma weight residual 118.50 116.72 1.78 9.90e-01 1.02e+00 3.23e+00 angle pdb=" CA ALA C 2 " pdb=" C ALA C 2 " pdb=" O ALA C 2 " ideal model delta sigma weight residual 120.55 118.79 1.76 1.06e+00 8.90e-01 2.77e+00 ... (remaining 7435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 3184 16.15 - 32.31: 246 32.31 - 48.46: 90 48.46 - 64.61: 16 64.61 - 80.77: 8 Dihedral angle restraints: 3544 sinusoidal: 1496 harmonic: 2048 Sorted by residual: dihedral pdb=" CG ARG F 55 " pdb=" CD ARG F 55 " pdb=" NE ARG F 55 " pdb=" CZ ARG F 55 " ideal model delta sinusoidal sigma weight residual 90.00 134.54 -44.54 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG E 55 " pdb=" CD ARG E 55 " pdb=" NE ARG E 55 " pdb=" CZ ARG E 55 " ideal model delta sinusoidal sigma weight residual 90.00 133.24 -43.24 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CG ARG H 55 " pdb=" CD ARG H 55 " pdb=" NE ARG H 55 " pdb=" CZ ARG H 55 " ideal model delta sinusoidal sigma weight residual 90.00 133.07 -43.07 2 1.50e+01 4.44e-03 9.95e+00 ... (remaining 3541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 459 0.021 - 0.043: 250 0.043 - 0.064: 133 0.064 - 0.085: 36 0.085 - 0.106: 18 Chirality restraints: 896 Sorted by residual: chirality pdb=" CA ARG F 33 " pdb=" N ARG F 33 " pdb=" C ARG F 33 " pdb=" CB ARG F 33 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.82e-01 chirality pdb=" CA ARG G 33 " pdb=" N ARG G 33 " pdb=" C ARG G 33 " pdb=" CB ARG G 33 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.79e-01 chirality pdb=" CA ARG D 33 " pdb=" N ARG D 33 " pdb=" C ARG D 33 " pdb=" CB ARG D 33 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.75e-01 ... (remaining 893 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 62 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO A 63 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 63 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 63 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 62 " 0.019 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO B 63 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 63 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 63 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 62 " 0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO E 63 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.016 5.00e-02 4.00e+02 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1929 2.89 - 3.39: 5586 3.39 - 3.90: 8971 3.90 - 4.40: 9379 4.40 - 4.90: 17066 Nonbonded interactions: 42931 Sorted by model distance: nonbonded pdb=" ND2 ASN A 36 " pdb=" OE2 GLU A 39 " model vdw 2.391 3.120 nonbonded pdb=" OG1 THR A 86 " pdb=" O LYS E 64 " model vdw 2.403 3.040 nonbonded pdb=" OD1 ASP B 3 " pdb=" N LYS B 4 " model vdw 2.408 3.120 nonbonded pdb=" OD1 ASP F 3 " pdb=" N LYS F 4 " model vdw 2.416 3.120 nonbonded pdb=" OD1 ASP H 3 " pdb=" N LYS H 4 " model vdw 2.430 3.120 ... (remaining 42926 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' } 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: 1.100 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.590 Find NCS groups from input model: 0.090 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:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 0.023 5568 Z= 0.108 Angle : 0.448 4.604 7440 Z= 0.268 Chirality : 0.034 0.106 896 Planarity : 0.003 0.029 936 Dihedral : 14.137 80.768 2216 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.34), residues: 696 helix: 1.62 (0.22), residues: 624 sheet: None (None), residues: 0 loop : -0.28 (0.65), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 33 TYR 0.010 0.002 TYR E 75 PHE 0.006 0.001 PHE F 13 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 5568) covalent geometry : angle 0.44771 ( 7440) hydrogen bonds : bond 0.13933 ( 416) hydrogen bonds : angle 4.82238 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.181 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 306 average time/residue: 0.7072 time to fit residues: 222.6619 Evaluate side-chains 275 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 0.0050 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.073783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.062376 restraints weight = 10144.986| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.06 r_work: 0.2585 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5568 Z= 0.150 Angle : 0.615 6.087 7440 Z= 0.330 Chirality : 0.037 0.106 896 Planarity : 0.005 0.038 936 Dihedral : 3.997 21.630 762 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 2.92 % Allowed : 22.24 % Favored : 74.84 % 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 are not related in a simple way. whole: 2.79 (0.34), residues: 696 helix: 2.08 (0.23), residues: 624 sheet: None (None), residues: 0 loop : -0.13 (0.71), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 15 TYR 0.008 0.001 TYR E 75 PHE 0.011 0.002 PHE H 13 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5568) covalent geometry : angle 0.61465 ( 7440) hydrogen bonds : bond 0.04298 ( 416) hydrogen bonds : angle 3.93893 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 274 time to evaluate : 0.143 Fit side-chains REVERT: A 4 LYS cc_start: 0.8269 (mtmt) cc_final: 0.7929 (mtmt) REVERT: A 8 GLU cc_start: 0.7970 (mp0) cc_final: 0.7758 (mp0) REVERT: B 80 ASP cc_start: 0.8387 (t0) cc_final: 0.8023 (t70) REVERT: C 80 ASP cc_start: 0.8194 (t0) cc_final: 0.7586 (t70) REVERT: D 33 ARG cc_start: 0.9022 (ttm110) cc_final: 0.8763 (mtp-110) REVERT: D 42 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8449 (mtpp) REVERT: E 33 ARG cc_start: 0.9049 (ttm110) cc_final: 0.8753 (mtp-110) REVERT: E 67 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8609 (mp10) REVERT: E 80 ASP cc_start: 0.8239 (t0) cc_final: 0.7728 (t70) REVERT: F 4 LYS cc_start: 0.8701 (mtpm) cc_final: 0.8273 (mtmm) REVERT: F 8 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8208 (mm-30) REVERT: F 33 ARG cc_start: 0.9046 (ttm-80) cc_final: 0.8828 (mtp-110) REVERT: F 86 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8983 (t) REVERT: G 33 ARG cc_start: 0.9066 (ttm-80) cc_final: 0.8805 (mtp-110) REVERT: H 37 LYS cc_start: 0.8723 (tppp) cc_final: 0.8466 (tptp) REVERT: H 45 ARG cc_start: 0.8748 (mmp80) cc_final: 0.8528 (mmt90) outliers start: 18 outliers final: 9 residues processed: 281 average time/residue: 0.6703 time to fit residues: 193.6608 Evaluate side-chains 281 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 270 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 80 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 16 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3000 r_free = 0.3000 target = 0.073741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.062696 restraints weight = 10174.875| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.06 r_work: 0.2601 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5568 Z= 0.131 Angle : 0.594 7.474 7440 Z= 0.315 Chirality : 0.037 0.122 896 Planarity : 0.005 0.038 936 Dihedral : 3.830 19.031 762 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 4.38 % Allowed : 25.97 % Favored : 69.64 % 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 are not related in a simple way. whole: 2.98 (0.34), residues: 696 helix: 2.20 (0.22), residues: 624 sheet: None (None), residues: 0 loop : -0.02 (0.76), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 45 TYR 0.006 0.001 TYR A 75 PHE 0.012 0.002 PHE D 13 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5568) covalent geometry : angle 0.59425 ( 7440) hydrogen bonds : bond 0.03681 ( 416) hydrogen bonds : angle 3.84838 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 274 time to evaluate : 0.154 Fit side-chains REVERT: B 80 ASP cc_start: 0.8324 (t0) cc_final: 0.7913 (t70) REVERT: C 33 ARG cc_start: 0.9039 (ttm-80) cc_final: 0.8811 (mmm-85) REVERT: C 67 GLN cc_start: 0.8275 (mp10) cc_final: 0.7962 (mp10) REVERT: C 80 ASP cc_start: 0.8222 (t0) cc_final: 0.7547 (t70) REVERT: D 33 ARG cc_start: 0.9011 (ttm110) cc_final: 0.8777 (mtp-110) REVERT: D 41 GLU cc_start: 0.9066 (tp30) cc_final: 0.8862 (mm-30) REVERT: E 33 ARG cc_start: 0.9038 (ttm110) cc_final: 0.8758 (mtp-110) REVERT: E 67 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8613 (mp10) REVERT: E 80 ASP cc_start: 0.8251 (t0) cc_final: 0.7709 (t70) REVERT: F 4 LYS cc_start: 0.8680 (mtpm) cc_final: 0.8280 (mtmm) REVERT: F 8 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8216 (mm-30) REVERT: F 33 ARG cc_start: 0.9032 (ttm-80) cc_final: 0.8809 (mtp-110) REVERT: F 41 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8803 (mm-30) REVERT: F 86 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8943 (t) REVERT: G 4 LYS cc_start: 0.8737 (mtpm) cc_final: 0.8444 (mtmm) REVERT: G 33 ARG cc_start: 0.8996 (ttm-80) cc_final: 0.8731 (mtp-110) REVERT: H 37 LYS cc_start: 0.8684 (tppp) cc_final: 0.8441 (tptp) REVERT: H 67 GLN cc_start: 0.8950 (mp10) cc_final: 0.8575 (mp10) outliers start: 27 outliers final: 10 residues processed: 283 average time/residue: 0.7536 time to fit residues: 219.0645 Evaluate side-chains 284 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 271 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain H residue 61 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.075174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.064007 restraints weight = 10187.987| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.07 r_work: 0.2623 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5568 Z= 0.124 Angle : 0.605 7.360 7440 Z= 0.317 Chirality : 0.035 0.113 896 Planarity : 0.005 0.038 936 Dihedral : 3.708 16.199 762 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 2.92 % Allowed : 27.76 % Favored : 69.32 % 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 are not related in a simple way. whole: 3.14 (0.34), residues: 696 helix: 2.30 (0.22), residues: 624 sheet: None (None), residues: 0 loop : 0.15 (0.82), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 15 TYR 0.006 0.001 TYR B 75 PHE 0.008 0.002 PHE C 13 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 5568) covalent geometry : angle 0.60501 ( 7440) hydrogen bonds : bond 0.03163 ( 416) hydrogen bonds : angle 3.83025 ( 1248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 275 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8280 (mtmt) REVERT: B 80 ASP cc_start: 0.8243 (t0) cc_final: 0.7807 (t70) REVERT: C 67 GLN cc_start: 0.8273 (mp10) cc_final: 0.7987 (mp10) REVERT: C 80 ASP cc_start: 0.8149 (t0) cc_final: 0.7453 (t70) REVERT: D 86 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8990 (t) REVERT: E 51 MET cc_start: 0.8735 (mpp) cc_final: 0.8520 (mpt) REVERT: E 67 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8603 (mp10) REVERT: E 80 ASP cc_start: 0.8217 (t0) cc_final: 0.7695 (t70) REVERT: F 4 LYS cc_start: 0.8661 (mtpm) cc_final: 0.8219 (mtmm) REVERT: F 8 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8193 (mm-30) REVERT: F 41 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8847 (mm-30) REVERT: F 86 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8968 (t) REVERT: G 8 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8263 (tp30) REVERT: G 67 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8606 (mp10) REVERT: H 8 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8107 (mm-30) REVERT: H 67 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8551 (mp10) outliers start: 18 outliers final: 10 residues processed: 282 average time/residue: 0.7662 time to fit residues: 221.9952 Evaluate side-chains 291 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 275 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 67 GLN Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 67 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.073479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.062347 restraints weight = 10545.142| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.12 r_work: 0.2591 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5568 Z= 0.140 Angle : 0.617 8.010 7440 Z= 0.322 Chirality : 0.036 0.111 896 Planarity : 0.005 0.041 936 Dihedral : 3.744 17.335 762 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 3.25 % Allowed : 31.98 % Favored : 64.77 % 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 are not related in a simple way. whole: 3.24 (0.34), residues: 696 helix: 2.37 (0.22), residues: 624 sheet: None (None), residues: 0 loop : 0.05 (0.84), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG E 33 TYR 0.006 0.001 TYR B 75 PHE 0.011 0.001 PHE C 13 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5568) covalent geometry : angle 0.61722 ( 7440) hydrogen bonds : bond 0.03554 ( 416) hydrogen bonds : angle 3.74472 ( 1248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 274 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 39 GLU cc_start: 0.8408 (mp0) cc_final: 0.7577 (mp0) REVERT: B 15 ARG cc_start: 0.8977 (ttm-80) cc_final: 0.8585 (mtm110) REVERT: B 67 GLN cc_start: 0.8502 (mp10) cc_final: 0.8300 (mp10) REVERT: B 80 ASP cc_start: 0.8330 (t0) cc_final: 0.7916 (t70) REVERT: C 15 ARG cc_start: 0.8973 (ttm-80) cc_final: 0.8668 (mtm110) REVERT: C 80 ASP cc_start: 0.8239 (t0) cc_final: 0.7520 (t70) REVERT: E 80 ASP cc_start: 0.8275 (t0) cc_final: 0.7753 (t70) REVERT: F 4 LYS cc_start: 0.8686 (mtpm) cc_final: 0.8247 (mtmm) REVERT: F 8 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8228 (mm-30) REVERT: F 41 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8832 (mm-30) REVERT: F 86 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8996 (t) REVERT: G 8 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8293 (tp30) REVERT: H 8 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8122 (mm-30) REVERT: H 39 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8009 (mt-10) REVERT: H 45 ARG cc_start: 0.8812 (mmp80) cc_final: 0.8581 (mmt90) REVERT: H 67 GLN cc_start: 0.8924 (mp10) cc_final: 0.8534 (mp10) REVERT: H 80 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7979 (m-30) outliers start: 20 outliers final: 12 residues processed: 283 average time/residue: 0.6932 time to fit residues: 201.6771 Evaluate side-chains 288 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 273 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 80 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 4 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.2986 r_free = 0.2986 target = 0.073130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.062045 restraints weight = 10429.674| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.12 r_work: 0.2581 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5568 Z= 0.150 Angle : 0.672 9.418 7440 Z= 0.349 Chirality : 0.037 0.126 896 Planarity : 0.005 0.046 936 Dihedral : 3.803 18.647 762 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 3.73 % Allowed : 31.66 % Favored : 64.61 % 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 are not related in a simple way. whole: 3.25 (0.34), residues: 696 helix: 2.40 (0.22), residues: 624 sheet: None (None), residues: 0 loop : -0.19 (0.82), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG E 15 TYR 0.005 0.001 TYR B 75 PHE 0.020 0.002 PHE H 13 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5568) covalent geometry : angle 0.67202 ( 7440) hydrogen bonds : bond 0.03575 ( 416) hydrogen bonds : angle 3.77444 ( 1248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 275 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8932 (tp30) cc_final: 0.8251 (tp30) REVERT: A 33 ARG cc_start: 0.9154 (mtp-110) cc_final: 0.8912 (ttm110) REVERT: B 37 LYS cc_start: 0.9020 (mmmm) cc_final: 0.8685 (tptp) REVERT: B 80 ASP cc_start: 0.8405 (t0) cc_final: 0.8024 (t70) REVERT: C 80 ASP cc_start: 0.8280 (t0) cc_final: 0.7594 (t70) REVERT: D 28 GLU cc_start: 0.8796 (tp30) cc_final: 0.8308 (tp30) REVERT: E 67 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8622 (mp10) REVERT: F 4 LYS cc_start: 0.8749 (mtpm) cc_final: 0.8255 (mtmm) REVERT: F 8 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8223 (mm-30) REVERT: F 41 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8898 (mm-30) REVERT: F 86 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.9113 (t) REVERT: G 8 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8347 (tp30) REVERT: G 67 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8609 (mp10) REVERT: H 8 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8185 (mm-30) REVERT: H 32 THR cc_start: 0.8772 (m) cc_final: 0.8532 (p) REVERT: H 37 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8527 (tptp) REVERT: H 39 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8102 (mt-10) REVERT: H 67 GLN cc_start: 0.8928 (mp10) cc_final: 0.8554 (mp10) REVERT: H 80 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8014 (m-30) outliers start: 23 outliers final: 13 residues processed: 285 average time/residue: 0.6559 time to fit residues: 192.2149 Evaluate side-chains 291 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 273 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 67 GLN Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 80 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 1 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.2913 r_free = 0.2913 target = 0.069136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.058220 restraints weight = 10762.812| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.13 r_work: 0.2489 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 5568 Z= 0.262 Angle : 0.744 10.130 7440 Z= 0.389 Chirality : 0.042 0.134 896 Planarity : 0.006 0.056 936 Dihedral : 4.146 17.198 762 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.71 % Allowed : 31.98 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.35), residues: 696 helix: 2.35 (0.22), residues: 624 sheet: None (None), residues: 0 loop : -0.35 (0.83), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG H 33 TYR 0.009 0.002 TYR H 75 PHE 0.005 0.001 PHE H 13 Details of bonding type rmsd covalent geometry : bond 0.00631 ( 5568) covalent geometry : angle 0.74362 ( 7440) hydrogen bonds : bond 0.05211 ( 416) hydrogen bonds : angle 3.77471 ( 1248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 269 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8914 (tp30) cc_final: 0.8261 (tp30) REVERT: B 37 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8650 (tptp) REVERT: B 80 ASP cc_start: 0.8498 (t0) cc_final: 0.8113 (t70) REVERT: C 80 ASP cc_start: 0.8441 (t0) cc_final: 0.7737 (t70) REVERT: D 4 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8341 (mtmt) REVERT: D 28 GLU cc_start: 0.8848 (tp30) cc_final: 0.8386 (tp30) REVERT: D 36 ASN cc_start: 0.8445 (p0) cc_final: 0.8101 (p0) REVERT: D 39 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8382 (mt-10) REVERT: E 37 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8670 (tppt) REVERT: F 4 LYS cc_start: 0.8757 (mtpm) cc_final: 0.8389 (mtmm) REVERT: F 8 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8334 (mm-30) REVERT: F 28 GLU cc_start: 0.8900 (tp30) cc_final: 0.8346 (tp30) REVERT: F 41 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8893 (mm-30) REVERT: G 8 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8387 (tp30) REVERT: H 8 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8274 (mm-30) REVERT: H 17 MET cc_start: 0.9061 (tpp) cc_final: 0.8854 (tpp) REVERT: H 32 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8597 (p) REVERT: H 39 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8093 (mt-10) REVERT: H 80 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8086 (m-30) outliers start: 29 outliers final: 13 residues processed: 281 average time/residue: 0.7274 time to fit residues: 210.0352 Evaluate side-chains 287 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 271 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 86 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.2947 r_free = 0.2947 target = 0.070844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.059742 restraints weight = 10352.081| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.09 r_work: 0.2545 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5568 Z= 0.176 Angle : 0.751 10.388 7440 Z= 0.390 Chirality : 0.039 0.131 896 Planarity : 0.006 0.054 936 Dihedral : 4.067 18.777 762 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.57 % Allowed : 33.12 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.34), residues: 696 helix: 2.36 (0.22), residues: 624 sheet: None (None), residues: 0 loop : -0.89 (0.78), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG B 33 TYR 0.005 0.001 TYR H 75 PHE 0.008 0.001 PHE D 13 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 5568) covalent geometry : angle 0.75100 ( 7440) hydrogen bonds : bond 0.04041 ( 416) hydrogen bonds : angle 3.81777 ( 1248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 276 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8892 (tp30) cc_final: 0.8249 (tp30) REVERT: A 39 GLU cc_start: 0.8390 (mp0) cc_final: 0.7621 (mp0) REVERT: B 37 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8760 (mmmt) REVERT: B 39 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: B 80 ASP cc_start: 0.8428 (t0) cc_final: 0.8051 (t70) REVERT: B 86 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8887 (t) REVERT: C 80 ASP cc_start: 0.8329 (t0) cc_final: 0.7643 (t70) REVERT: C 86 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8979 (t) REVERT: D 28 GLU cc_start: 0.8856 (tp30) cc_final: 0.8390 (tp30) REVERT: D 36 ASN cc_start: 0.8283 (p0) cc_final: 0.7832 (p0) REVERT: D 39 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8344 (mp0) REVERT: F 4 LYS cc_start: 0.8716 (mtpm) cc_final: 0.8361 (mmtm) REVERT: F 8 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8283 (mm-30) REVERT: F 28 GLU cc_start: 0.8855 (tp30) cc_final: 0.8281 (tp30) REVERT: F 41 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8864 (mm-30) REVERT: G 8 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8408 (tp30) REVERT: H 8 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8256 (mm-30) REVERT: H 32 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8460 (p) REVERT: H 39 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7992 (mt-10) REVERT: H 80 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8062 (m-30) outliers start: 22 outliers final: 11 residues processed: 282 average time/residue: 0.7678 time to fit residues: 222.4191 Evaluate side-chains 291 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 274 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 80 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.2955 r_free = 0.2955 target = 0.071330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.060411 restraints weight = 10595.645| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.10 r_work: 0.2539 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5568 Z= 0.171 Angle : 0.757 10.093 7440 Z= 0.394 Chirality : 0.039 0.130 896 Planarity : 0.006 0.059 936 Dihedral : 4.047 17.631 762 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.08 % Allowed : 33.93 % Favored : 62.99 % 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 are not related in a simple way. whole: 3.13 (0.34), residues: 696 helix: 2.40 (0.22), residues: 624 sheet: None (None), residues: 0 loop : -1.03 (0.78), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 33 TYR 0.006 0.001 TYR H 75 PHE 0.004 0.001 PHE B 13 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 5568) covalent geometry : angle 0.75725 ( 7440) hydrogen bonds : bond 0.03969 ( 416) hydrogen bonds : angle 3.82298 ( 1248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 273 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8899 (tp30) cc_final: 0.8267 (tp30) REVERT: A 39 GLU cc_start: 0.8454 (mp0) cc_final: 0.7654 (mp0) REVERT: B 37 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8761 (mmmt) REVERT: B 80 ASP cc_start: 0.8407 (t0) cc_final: 0.8062 (t70) REVERT: B 86 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8940 (t) REVERT: C 80 ASP cc_start: 0.8311 (t0) cc_final: 0.7650 (t70) REVERT: C 86 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8984 (t) REVERT: D 28 GLU cc_start: 0.8842 (tp30) cc_final: 0.8315 (tp30) REVERT: D 36 ASN cc_start: 0.8250 (p0) cc_final: 0.7841 (p0) REVERT: D 37 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8615 (mmmt) REVERT: E 37 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8647 (mmmt) REVERT: E 41 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8890 (mm-30) REVERT: E 80 ASP cc_start: 0.8321 (t0) cc_final: 0.7819 (t70) REVERT: F 4 LYS cc_start: 0.8744 (mtpm) cc_final: 0.8379 (mmtm) REVERT: F 8 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8278 (mm-30) REVERT: F 28 GLU cc_start: 0.8858 (tp30) cc_final: 0.8292 (tp30) REVERT: F 41 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8872 (mm-30) REVERT: G 8 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8410 (tp30) REVERT: H 8 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8262 (mm-30) REVERT: H 32 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8440 (p) REVERT: H 39 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7996 (mt-10) REVERT: H 51 MET cc_start: 0.8490 (mpt) cc_final: 0.8173 (mpt) REVERT: H 80 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8083 (m-30) outliers start: 19 outliers final: 13 residues processed: 279 average time/residue: 0.7119 time to fit residues: 204.3491 Evaluate side-chains 291 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 272 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 80 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.2984 r_free = 0.2984 target = 0.072910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.061895 restraints weight = 10567.049| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.10 r_work: 0.2595 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5568 Z= 0.161 Angle : 0.777 9.897 7440 Z= 0.406 Chirality : 0.038 0.126 896 Planarity : 0.006 0.061 936 Dihedral : 4.039 16.790 762 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.76 % Allowed : 34.90 % Favored : 62.34 % 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 are not related in a simple way. whole: 3.09 (0.34), residues: 696 helix: 2.37 (0.22), residues: 624 sheet: None (None), residues: 0 loop : -1.01 (0.79), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 33 TYR 0.005 0.001 TYR F 75 PHE 0.018 0.002 PHE F 13 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 5568) covalent geometry : angle 0.77702 ( 7440) hydrogen bonds : bond 0.03612 ( 416) hydrogen bonds : angle 3.93212 ( 1248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 275 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8879 (tp30) cc_final: 0.8277 (tp30) REVERT: A 39 GLU cc_start: 0.8486 (mp0) cc_final: 0.7675 (mp0) REVERT: B 37 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8778 (mmmt) REVERT: B 80 ASP cc_start: 0.8400 (t0) cc_final: 0.8038 (t70) REVERT: B 86 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8918 (t) REVERT: C 80 ASP cc_start: 0.8230 (t0) cc_final: 0.7582 (t70) REVERT: D 28 GLU cc_start: 0.8841 (tp30) cc_final: 0.8333 (tp30) REVERT: D 39 GLU cc_start: 0.8618 (mp0) cc_final: 0.8157 (mp0) REVERT: E 37 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8597 (mmmt) REVERT: E 67 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8583 (mp10) REVERT: F 4 LYS cc_start: 0.8736 (mtpm) cc_final: 0.8372 (mmtm) REVERT: F 8 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8263 (mm-30) REVERT: F 28 GLU cc_start: 0.8828 (tp30) cc_final: 0.8257 (tp30) REVERT: F 41 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8889 (mm-30) REVERT: G 8 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8458 (tp30) REVERT: G 39 GLU cc_start: 0.8656 (mp0) cc_final: 0.7899 (mp0) REVERT: G 45 ARG cc_start: 0.8724 (mmt90) cc_final: 0.8517 (mmt90) REVERT: H 8 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8258 (mm-30) REVERT: H 32 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8461 (p) REVERT: H 37 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8517 (tptp) REVERT: H 39 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7971 (mt-10) REVERT: H 51 MET cc_start: 0.8478 (mpt) cc_final: 0.8164 (mpt) REVERT: H 80 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7983 (m-30) outliers start: 17 outliers final: 11 residues processed: 279 average time/residue: 0.6853 time to fit residues: 196.4548 Evaluate side-chains 287 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 271 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 80 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 0.0570 chunk 48 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- 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 = 0.2963 r_free = 0.2963 target = 0.071627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.060765 restraints weight = 10634.928| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.10 r_work: 0.2569 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5568 Z= 0.183 Angle : 0.792 9.295 7440 Z= 0.416 Chirality : 0.040 0.131 896 Planarity : 0.007 0.065 936 Dihedral : 4.114 18.945 762 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.76 % Allowed : 35.88 % Favored : 61.36 % 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 are not related in a simple way. whole: 3.11 (0.34), residues: 696 helix: 2.40 (0.22), residues: 624 sheet: None (None), residues: 0 loop : -1.17 (0.75), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 33 TYR 0.006 0.001 TYR H 75 PHE 0.035 0.003 PHE E 13 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 5568) covalent geometry : angle 0.79207 ( 7440) hydrogen bonds : bond 0.04228 ( 416) hydrogen bonds : angle 3.92398 ( 1248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3019.37 seconds wall clock time: 51 minutes 54.43 seconds (3114.43 seconds total)