Starting phenix.real_space_refine on Tue Aug 4 17:25:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yyg_73644/08_2026/9yyg_73644.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yyg_73644/08_2026/9yyg_73644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yyg_73644/08_2026/9yyg_73644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yyg_73644/08_2026/9yyg_73644.map" model { file = "/net/cci-nas-00/data/ceres_data/9yyg_73644/08_2026/9yyg_73644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yyg_73644/08_2026/9yyg_73644.cif" } resolution = 2.8 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= 0.001 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: 5 Type Number sf(0) Gaussians P 131 5.49 5 S 2 5.16 5 C 2926 2.51 5 N 995 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5410 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2626 Classifications: {'peptide': 322} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 312} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2470 Classifications: {'DNA': 1, 'RNA': 115} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 45} Link IDs: {'rna2p': 18, 'rna3p': 97} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 151 Classifications: {'DNA': 8} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 7} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 163 Classifications: {'DNA': 9} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 8} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DT%5*END:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 1.14, per 1000 atoms: 0.21 Number of scatterers: 5410 At special positions: 0 Unit cell: (80.56, 92.432, 97.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 2 16.00 P 131 15.00 O 1356 8.00 N 995 7.00 C 2926 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: 0.51 Conformation dependent library (CDL) restraints added in 103.6 milliseconds 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 602 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 2 sheets defined 52.8% alpha, 19.6% beta 48 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 14 through 45 Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 68 through 74 removed outlier: 3.634A pdb=" N LEU A 71 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A 73 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 100 removed outlier: 3.975A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 232 removed outlier: 4.089A pdb=" N LYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LYS A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 271 Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 361 through 377 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.599A pdb=" N GLU A 116 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL A 154 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU A 174 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 156 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N HIS A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR A 167 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 10 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 143 " --> pdb=" O TYR A 12 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 209 removed outlier: 3.614A pdb=" N ASP A 191 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 186 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 277 " --> pdb=" O ALA A 319 " (cutoff:3.500A) 170 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 118 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 0.76 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 960 1.33 - 1.45: 2042 1.45 - 1.57: 2518 1.57 - 1.69: 260 1.69 - 1.81: 4 Bond restraints: 5784 Sorted by residual: bond pdb=" C1' DT C -6 " pdb=" N1 DT C -6 " ideal model delta sigma weight residual 1.468 1.545 -0.077 1.40e-02 5.10e+03 3.06e+01 bond pdb=" C1' DA D 6 " pdb=" N9 DA D 6 " ideal model delta sigma weight residual 1.468 1.399 0.069 1.40e-02 5.10e+03 2.43e+01 bond pdb=" C3' DA D 4 " pdb=" C2' DA D 4 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.18e+00 bond pdb=" C3' DA D 6 " pdb=" C2' DA D 6 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.56e+00 bond pdb=" C HIS A 34 " pdb=" O HIS A 34 " ideal model delta sigma weight residual 1.236 1.267 -0.031 1.15e-02 7.56e+03 7.17e+00 ... (remaining 5779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 7845 1.50 - 2.99: 523 2.99 - 4.49: 41 4.49 - 5.98: 7 5.98 - 7.48: 3 Bond angle restraints: 8419 Sorted by residual: angle pdb=" C1' C B -25 " pdb=" N1 C B -25 " pdb=" C2 C B -25 " ideal model delta sigma weight residual 118.80 123.81 -5.01 1.10e+00 8.26e-01 2.08e+01 angle pdb=" N HIS A 34 " pdb=" CA HIS A 34 " pdb=" C HIS A 34 " ideal model delta sigma weight residual 110.97 115.65 -4.68 1.09e+00 8.42e-01 1.85e+01 angle pdb=" N3 DT C -3 " pdb=" C4 DT C -3 " pdb=" O4 DT C -3 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" O5' A B 2 " pdb=" C5' A B 2 " pdb=" C4' A B 2 " ideal model delta sigma weight residual 109.40 112.68 -3.28 8.00e-01 1.56e+00 1.68e+01 angle pdb=" N3 DT C -4 " pdb=" C4 DT C -4 " pdb=" O4 DT C -4 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 8414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 3222 35.46 - 70.93: 368 70.93 - 106.39: 31 106.39 - 141.85: 0 141.85 - 177.32: 2 Dihedral angle restraints: 3623 sinusoidal: 2694 harmonic: 929 Sorted by residual: dihedral pdb=" O4' U B -58 " pdb=" C1' U B -58 " pdb=" N1 U B -58 " pdb=" C2 U B -58 " ideal model delta sinusoidal sigma weight residual 200.00 22.68 177.32 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C B -56 " pdb=" C1' C B -56 " pdb=" N1 C B -56 " pdb=" C2 C B -56 " ideal model delta sinusoidal sigma weight residual -128.00 -41.60 -86.40 1 1.70e+01 3.46e-03 3.11e+01 dihedral pdb=" O4' G B -55 " pdb=" C1' G B -55 " pdb=" N9 G B -55 " pdb=" C4 G B -55 " ideal model delta sinusoidal sigma weight residual 68.00 147.94 -79.94 1 1.70e+01 3.46e-03 2.74e+01 ... (remaining 3620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 575 0.035 - 0.070: 275 0.070 - 0.106: 151 0.106 - 0.141: 19 0.141 - 0.176: 3 Chirality restraints: 1023 Sorted by residual: chirality pdb=" C1' DA D 6 " pdb=" O4' DA D 6 " pdb=" C2' DA D 6 " pdb=" N9 DA D 6 " both_signs ideal model delta sigma weight residual False 2.43 2.26 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CG LEU A 192 " pdb=" CB LEU A 192 " pdb=" CD1 LEU A 192 " pdb=" CD2 LEU A 192 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" C3' C B 5 " pdb=" C4' C B 5 " pdb=" O3' C B 5 " pdb=" C2' C B 5 " both_signs ideal model delta sigma weight residual False -2.48 -2.63 0.15 2.00e-01 2.50e+01 5.80e-01 ... (remaining 1020 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B -88 " 0.030 2.00e-02 2.50e+03 1.45e-02 5.76e+00 pdb=" N9 A B -88 " -0.036 2.00e-02 2.50e+03 pdb=" C8 A B -88 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B -88 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A B -88 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B -88 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A B -88 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A B -88 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B -88 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A B -88 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A B -88 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B -92 " 0.029 2.00e-02 2.50e+03 1.55e-02 5.42e+00 pdb=" N1 C B -92 " -0.034 2.00e-02 2.50e+03 pdb=" C2 C B -92 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C B -92 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C B -92 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C B -92 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C B -92 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C B -92 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C B -92 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA C -5 " 0.029 2.00e-02 2.50e+03 1.27e-02 4.47e+00 pdb=" N9 DA C -5 " -0.005 2.00e-02 2.50e+03 pdb=" C8 DA C -5 " -0.010 2.00e-02 2.50e+03 pdb=" N7 DA C -5 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DA C -5 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DA C -5 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA C -5 " 0.023 2.00e-02 2.50e+03 pdb=" N1 DA C -5 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA C -5 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DA C -5 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DA C -5 " -0.009 2.00e-02 2.50e+03 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 886 2.76 - 3.30: 4576 3.30 - 3.83: 10334 3.83 - 4.37: 11791 4.37 - 4.90: 17245 Nonbonded interactions: 44832 Sorted by model distance: nonbonded pdb=" NH2 ARG A 238 " pdb=" N7 G B -33 " model vdw 2.228 3.200 nonbonded pdb=" OE2 GLU A 308 " pdb=" NZ LYS A 320 " model vdw 2.233 3.120 nonbonded pdb=" O5' U B -58 " pdb=" O2 U B -58 " model vdw 2.290 3.040 nonbonded pdb=" O2' G B -55 " pdb=" O5' G B -54 " model vdw 2.303 3.040 nonbonded pdb=" O2' G B 1 " pdb=" OP2 A B 2 " model vdw 2.329 3.040 ... (remaining 44827 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.690 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.610 Find NCS groups from input model: 0.010 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.005 0.077 5784 Z= 0.439 Angle : 0.734 7.481 8419 Z= 0.635 Chirality : 0.048 0.176 1023 Planarity : 0.004 0.040 586 Dihedral : 22.979 177.318 3021 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.74 % Allowed : 20.66 % Favored : 78.60 % 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: 1.68 (0.48), residues: 316 helix: 2.62 (0.40), residues: 162 sheet: -0.48 (0.67), residues: 60 loop : -0.46 (0.64), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 88 TYR 0.023 0.002 TYR A 309 PHE 0.016 0.002 PHE A 30 TRP 0.006 0.001 TRP A 239 HIS 0.003 0.002 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.44 ( 5784) covalent geometry : angle 0.73407 / 0.63 ( 8419) hydrogen bonds : bond 0.14634 / 10.01 ( 288) hydrogen bonds : angle 5.27882 / 3.94 ( 687) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.078 Fit side-chains REVERT: A 116 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7718 (mt-10) REVERT: A 219 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 300 TRP cc_start: 0.7731 (m-90) cc_final: 0.7152 (m-90) REVERT: A 302 GLU cc_start: 0.7300 (tt0) cc_final: 0.7095 (tt0) outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 0.7547 time to fit residues: 44.0868 Evaluate side-chains 54 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 368 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.133536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.113251 restraints weight = 8656.799| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.49 r_work: 0.3438 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5784 Z= 0.158 Angle : 0.545 6.039 8419 Z= 0.324 Chirality : 0.038 0.379 1023 Planarity : 0.005 0.029 586 Dihedral : 24.095 174.798 2342 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.06 % Allowed : 18.08 % Favored : 77.86 % 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: 2.01 (0.48), residues: 316 helix: 2.92 (0.39), residues: 165 sheet: -0.64 (0.57), residues: 71 loop : -0.14 (0.72), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 88 TYR 0.021 0.002 TYR A 309 PHE 0.013 0.002 PHE A 109 TRP 0.009 0.002 TRP A 300 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 ( 5784) covalent geometry : angle 0.54524 / 0.32 ( 8419) hydrogen bonds : bond 0.07409 / 5.21 ( 288) hydrogen bonds : angle 4.07015 / 3.01 ( 687) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.087 Fit side-chains REVERT: A 116 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7562 (mt-10) REVERT: A 300 TRP cc_start: 0.7848 (m-90) cc_final: 0.7204 (m-90) outliers start: 11 outliers final: 7 residues processed: 55 average time/residue: 0.8101 time to fit residues: 45.8266 Evaluate side-chains 56 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 0.1980 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.130292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.109748 restraints weight = 8587.361| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.47 r_work: 0.3393 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5784 Z= 0.252 Angle : 0.607 6.545 8419 Z= 0.349 Chirality : 0.043 0.357 1023 Planarity : 0.005 0.034 586 Dihedral : 23.997 168.796 2338 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.90 % Allowed : 17.71 % Favored : 76.38 % 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: 1.73 (0.47), residues: 316 helix: 2.66 (0.38), residues: 164 sheet: -0.71 (0.57), residues: 74 loop : -0.15 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 243 TYR 0.036 0.003 TYR A 309 PHE 0.027 0.003 PHE A 109 TRP 0.006 0.002 TRP A 70 HIS 0.006 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.25 ( 5784) covalent geometry : angle 0.60677 / 0.35 ( 8419) hydrogen bonds : bond 0.08397 / 5.88 ( 288) hydrogen bonds : angle 4.04825 / 3.00 ( 687) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.094 Fit side-chains REVERT: A 70 TRP cc_start: 0.7460 (OUTLIER) cc_final: 0.6027 (p-90) REVERT: A 116 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7556 (mt-10) REVERT: A 233 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7813 (mttm) REVERT: A 260 PHE cc_start: 0.8522 (t80) cc_final: 0.8260 (t80) outliers start: 16 outliers final: 10 residues processed: 59 average time/residue: 0.7032 time to fit residues: 42.6404 Evaluate side-chains 63 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.133413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113145 restraints weight = 8599.692| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.48 r_work: 0.3445 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5784 Z= 0.140 Angle : 0.510 7.601 8419 Z= 0.302 Chirality : 0.037 0.363 1023 Planarity : 0.004 0.034 586 Dihedral : 23.955 167.235 2338 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.69 % Allowed : 21.77 % Favored : 74.54 % 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: 2.07 (0.48), residues: 316 helix: 2.99 (0.39), residues: 164 sheet: -0.65 (0.57), residues: 74 loop : -0.02 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 23 TYR 0.023 0.002 TYR A 309 PHE 0.012 0.002 PHE A 109 TRP 0.004 0.001 TRP A 300 HIS 0.003 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 ( 5784) covalent geometry : angle 0.51036 / 0.30 ( 8419) hydrogen bonds : bond 0.06676 / 4.75 ( 288) hydrogen bonds : angle 3.79955 / 2.80 ( 687) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.132 Fit side-chains REVERT: A 116 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7460 (mt-10) REVERT: A 302 GLU cc_start: 0.7489 (tt0) cc_final: 0.6940 (mt-10) outliers start: 10 outliers final: 6 residues processed: 56 average time/residue: 0.7152 time to fit residues: 41.2691 Evaluate side-chains 53 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 368 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.132391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.112149 restraints weight = 8697.239| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.43 r_work: 0.3434 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5784 Z= 0.180 Angle : 0.533 6.134 8419 Z= 0.311 Chirality : 0.037 0.359 1023 Planarity : 0.004 0.028 586 Dihedral : 23.892 167.005 2338 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.17 % Allowed : 19.93 % Favored : 74.91 % 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: 2.04 (0.48), residues: 316 helix: 2.95 (0.38), residues: 164 sheet: -0.62 (0.58), residues: 74 loop : -0.04 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 23 TYR 0.026 0.002 TYR A 309 PHE 0.018 0.002 PHE A 109 TRP 0.007 0.002 TRP A 300 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.18 ( 5784) covalent geometry : angle 0.53253 / 0.31 ( 8419) hydrogen bonds : bond 0.06882 / 4.86 ( 288) hydrogen bonds : angle 3.79390 / 2.81 ( 687) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.122 Fit side-chains REVERT: A 70 TRP cc_start: 0.7440 (OUTLIER) cc_final: 0.6004 (p-90) REVERT: A 116 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7475 (mt-10) outliers start: 14 outliers final: 11 residues processed: 58 average time/residue: 0.7060 time to fit residues: 42.0598 Evaluate side-chains 58 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 368 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.0270 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.133929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.113789 restraints weight = 8549.955| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.45 r_work: 0.3458 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5784 Z= 0.138 Angle : 0.505 7.672 8419 Z= 0.296 Chirality : 0.036 0.356 1023 Planarity : 0.004 0.034 586 Dihedral : 23.861 166.409 2338 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.43 % Allowed : 21.03 % Favored : 74.54 % 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: 2.27 (0.47), residues: 316 helix: 3.09 (0.38), residues: 164 sheet: -0.10 (0.59), residues: 63 loop : -0.35 (0.65), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 252 TYR 0.022 0.002 TYR A 309 PHE 0.013 0.002 PHE A 109 TRP 0.007 0.001 TRP A 300 HIS 0.003 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 ( 5784) covalent geometry : angle 0.50522 / 0.30 ( 8419) hydrogen bonds : bond 0.06170 / 4.39 ( 288) hydrogen bonds : angle 3.68434 / 2.72 ( 687) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.129 Fit side-chains REVERT: A 116 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7472 (tt0) REVERT: A 302 GLU cc_start: 0.7403 (tt0) cc_final: 0.7183 (tt0) outliers start: 12 outliers final: 10 residues processed: 57 average time/residue: 0.7203 time to fit residues: 42.2394 Evaluate side-chains 56 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 368 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.130944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110252 restraints weight = 8636.548| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.50 r_work: 0.3398 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5784 Z= 0.257 Angle : 0.605 7.337 8419 Z= 0.342 Chirality : 0.042 0.363 1023 Planarity : 0.005 0.035 586 Dihedral : 23.856 166.765 2338 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.90 % Allowed : 19.93 % Favored : 74.17 % 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: 1.84 (0.47), residues: 316 helix: 2.75 (0.38), residues: 164 sheet: -0.60 (0.58), residues: 73 loop : -0.19 (0.71), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 252 TYR 0.034 0.003 TYR A 309 PHE 0.026 0.003 PHE A 109 TRP 0.008 0.002 TRP A 300 HIS 0.005 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.26 ( 5784) covalent geometry : angle 0.60489 / 0.34 ( 8419) hydrogen bonds : bond 0.07729 / 5.39 ( 288) hydrogen bonds : angle 3.83986 / 2.85 ( 687) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.081 Fit side-chains REVERT: A 70 TRP cc_start: 0.7502 (OUTLIER) cc_final: 0.5625 (p-90) REVERT: A 73 GLU cc_start: 0.7203 (mp0) cc_final: 0.6813 (mp0) REVERT: A 116 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7532 (mt-10) REVERT: A 208 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8006 (ttpt) REVERT: A 260 PHE cc_start: 0.8504 (t80) cc_final: 0.8234 (t80) outliers start: 16 outliers final: 9 residues processed: 60 average time/residue: 0.6195 time to fit residues: 38.2700 Evaluate side-chains 61 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 39 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.133012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112453 restraints weight = 8604.065| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.49 r_work: 0.3433 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5784 Z= 0.167 Angle : 0.537 9.304 8419 Z= 0.310 Chirality : 0.037 0.358 1023 Planarity : 0.004 0.037 586 Dihedral : 23.814 166.199 2338 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.80 % Allowed : 21.03 % Favored : 74.17 % 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: 2.18 (0.47), residues: 316 helix: 3.00 (0.38), residues: 164 sheet: -0.04 (0.59), residues: 63 loop : -0.42 (0.65), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 252 TYR 0.025 0.002 TYR A 309 PHE 0.016 0.002 PHE A 109 TRP 0.005 0.001 TRP A 300 HIS 0.003 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 ( 5784) covalent geometry : angle 0.53725 / 0.31 ( 8419) hydrogen bonds : bond 0.06610 / 4.68 ( 288) hydrogen bonds : angle 3.70393 / 2.73 ( 687) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.087 Fit side-chains REVERT: A 73 GLU cc_start: 0.7153 (mp0) cc_final: 0.6757 (mp0) REVERT: A 208 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7931 (ttpt) REVERT: A 302 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7247 (tt0) outliers start: 13 outliers final: 9 residues processed: 56 average time/residue: 0.7516 time to fit residues: 43.2099 Evaluate side-chains 60 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.132709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112328 restraints weight = 8628.413| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.48 r_work: 0.3427 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5784 Z= 0.174 Angle : 0.540 8.875 8419 Z= 0.310 Chirality : 0.037 0.358 1023 Planarity : 0.004 0.037 586 Dihedral : 23.754 166.195 2338 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.43 % Allowed : 21.77 % Favored : 73.80 % 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: 2.05 (0.48), residues: 316 helix: 2.97 (0.38), residues: 164 sheet: -0.65 (0.58), residues: 74 loop : -0.05 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 252 TYR 0.026 0.002 TYR A 309 PHE 0.018 0.002 PHE A 109 TRP 0.005 0.001 TRP A 300 HIS 0.004 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 ( 5784) covalent geometry : angle 0.53969 / 0.31 ( 8419) hydrogen bonds : bond 0.06549 / 4.59 ( 288) hydrogen bonds : angle 3.66836 / 2.70 ( 687) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.105 Fit side-chains REVERT: A 73 GLU cc_start: 0.7189 (mp0) cc_final: 0.6797 (mp0) REVERT: A 302 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7259 (tt0) outliers start: 12 outliers final: 7 residues processed: 59 average time/residue: 0.6894 time to fit residues: 41.8009 Evaluate side-chains 58 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.134485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114071 restraints weight = 8587.282| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.48 r_work: 0.3454 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5784 Z= 0.134 Angle : 0.516 8.653 8419 Z= 0.298 Chirality : 0.035 0.353 1023 Planarity : 0.004 0.035 586 Dihedral : 23.730 165.835 2338 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.95 % Allowed : 23.25 % Favored : 73.80 % 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: 2.24 (0.47), residues: 316 helix: 3.08 (0.39), residues: 164 sheet: -0.14 (0.58), residues: 63 loop : -0.35 (0.66), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 252 TYR 0.020 0.002 TYR A 309 PHE 0.012 0.002 PHE A 109 TRP 0.005 0.001 TRP A 300 HIS 0.002 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 5784) covalent geometry : angle 0.51618 / 0.30 ( 8419) hydrogen bonds : bond 0.05868 / 4.13 ( 288) hydrogen bonds : angle 3.56630 / 2.61 ( 687) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.119 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 50 average time/residue: 0.7480 time to fit residues: 38.4439 Evaluate side-chains 53 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.0870 chunk 41 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.134363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.114283 restraints weight = 8487.710| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.45 r_work: 0.3458 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5784 Z= 0.143 Angle : 0.526 8.455 8419 Z= 0.301 Chirality : 0.035 0.351 1023 Planarity : 0.004 0.036 586 Dihedral : 23.719 165.867 2338 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.32 % Allowed : 23.25 % Favored : 73.43 % 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 are not related in a simple way. whole: 2.22 (0.47), residues: 316 helix: 3.02 (0.39), residues: 164 sheet: -0.14 (0.58), residues: 63 loop : -0.27 (0.67), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 252 TYR 0.021 0.002 TYR A 309 PHE 0.014 0.002 PHE A 109 TRP 0.005 0.001 TRP A 239 HIS 0.003 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 5784) covalent geometry : angle 0.52600 / 0.30 ( 8419) hydrogen bonds : bond 0.05897 / 4.16 ( 288) hydrogen bonds : angle 3.56901 / 2.61 ( 687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1724.79 seconds wall clock time: 30 minutes 1.92 seconds (1801.92 seconds total)