Starting phenix.real_space_refine on Thu Jul 2 04:36:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ifu_35423/07_2026/8ifu_35423_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifu_35423/07_2026/8ifu_35423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ifu_35423/07_2026/8ifu_35423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifu_35423/07_2026/8ifu_35423.map" model { file = "/net/cci-nas-00/data/ceres_data/8ifu_35423/07_2026/8ifu_35423_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifu_35423/07_2026/8ifu_35423_neut.cif" } resolution = 2.37 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= -0.000 sd= 0.029 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 42 5.16 5 Na 48 4.78 5 C 4548 2.51 5 N 978 2.21 5 O 1110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6732 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2095 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 14, 'TRANS': 244} Chain: "B" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2095 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 14, 'TRANS': 244} Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2095 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 14, 'TRANS': 244} Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 122 Ad-hoc single atom residues: {' NA': 16} Unusual residues: {'L9Q': 2, 'RET': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 16 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 122 Ad-hoc single atom residues: {' NA': 16} Unusual residues: {'L9Q': 2, 'RET': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 16 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 122 Ad-hoc single atom residues: {' NA': 16} Unusual residues: {'L9Q': 2, 'RET': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 16 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 1.82, per 1000 atoms: 0.27 Number of scatterers: 6732 At special positions: 0 Unit cell: (74.67, 74.67, 80.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 6 15.00 Na 48 11.00 O 1110 8.00 N 978 7.00 C 4548 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 303.4 milliseconds 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1416 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 72.6% 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 21 through 50 removed outlier: 4.076A pdb=" N GLY A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 103 through 121 removed outlier: 3.730A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 150 through 178 Proline residue: A 164 - end of helix removed outlier: 3.859A pdb=" N GLN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 removed outlier: 3.620A pdb=" N ILE A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 194 " --> pdb=" O TRP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 removed outlier: 3.921A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 50 removed outlier: 4.076A pdb=" N GLY B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 103 through 121 removed outlier: 3.730A pdb=" N PHE B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 150 through 178 Proline residue: B 164 - end of helix removed outlier: 3.858A pdb=" N GLN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 removed outlier: 3.620A pdb=" N ILE B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 194 " --> pdb=" O TRP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 removed outlier: 3.921A pdb=" N ILE B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 50 removed outlier: 4.077A pdb=" N GLY C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 103 through 121 removed outlier: 3.730A pdb=" N PHE C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 150 through 178 Proline residue: C 164 - end of helix removed outlier: 3.859A pdb=" N GLN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 196 removed outlier: 3.619A pdb=" N ILE C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 194 " --> pdb=" O TRP C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 removed outlier: 3.921A pdb=" N ILE C 204 " --> pdb=" O PRO C 200 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 405 hydrogen bonds defined for protein. 1206 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: 1.02 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1026 1.32 - 1.44: 2241 1.44 - 1.56: 3561 1.56 - 1.69: 18 1.69 - 1.81: 54 Bond restraints: 6900 Sorted by residual: bond pdb=" C39 L9Q B 301 " pdb=" C40 L9Q B 301 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" C39 L9Q C 302 " pdb=" C40 L9Q C 302 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C39 L9Q A 319 " pdb=" C40 L9Q A 319 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C39 L9Q B 319 " pdb=" C40 L9Q B 319 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" C39 L9Q C 301 " pdb=" C40 L9Q C 301 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.89e+01 ... (remaining 6895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.76: 9171 5.76 - 11.51: 126 11.51 - 17.27: 21 17.27 - 23.03: 6 23.03 - 28.78: 6 Bond angle restraints: 9330 Sorted by residual: angle pdb=" C17 RET C 303 " pdb=" C1 RET C 303 " pdb=" C6 RET C 303 " ideal model delta sigma weight residual 110.87 82.09 28.78 3.00e+00 1.11e-01 9.20e+01 angle pdb=" C17 RET B 302 " pdb=" C1 RET B 302 " pdb=" C6 RET B 302 " ideal model delta sigma weight residual 110.87 82.09 28.78 3.00e+00 1.11e-01 9.20e+01 angle pdb=" C17 RET A 301 " pdb=" C1 RET A 301 " pdb=" C6 RET A 301 " ideal model delta sigma weight residual 110.87 82.10 28.77 3.00e+00 1.11e-01 9.20e+01 angle pdb=" C16 RET B 302 " pdb=" C1 RET B 302 " pdb=" C17 RET B 302 " ideal model delta sigma weight residual 109.83 84.95 24.88 3.00e+00 1.11e-01 6.88e+01 angle pdb=" C16 RET A 301 " pdb=" C1 RET A 301 " pdb=" C17 RET A 301 " ideal model delta sigma weight residual 109.83 84.95 24.88 3.00e+00 1.11e-01 6.88e+01 ... (remaining 9325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 3527 35.19 - 70.38: 301 70.38 - 105.57: 27 105.57 - 140.75: 9 140.75 - 175.94: 18 Dihedral angle restraints: 3882 sinusoidal: 1653 harmonic: 2229 Sorted by residual: dihedral pdb=" C GLU B 248 " pdb=" N GLU B 248 " pdb=" CA GLU B 248 " pdb=" CB GLU B 248 " ideal model delta harmonic sigma weight residual -122.60 -134.82 12.22 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" C GLU C 248 " pdb=" N GLU C 248 " pdb=" CA GLU C 248 " pdb=" CB GLU C 248 " ideal model delta harmonic sigma weight residual -122.60 -134.80 12.20 0 2.50e+00 1.60e-01 2.38e+01 dihedral pdb=" C GLU A 248 " pdb=" N GLU A 248 " pdb=" CA GLU A 248 " pdb=" CB GLU A 248 " ideal model delta harmonic sigma weight residual -122.60 -134.80 12.20 0 2.50e+00 1.60e-01 2.38e+01 ... (remaining 3879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 620 0.116 - 0.232: 255 0.232 - 0.348: 37 0.348 - 0.463: 15 0.463 - 0.579: 9 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA GLU A 248 " pdb=" N GLU A 248 " pdb=" C GLU A 248 " pdb=" CB GLU A 248 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" CA GLU C 248 " pdb=" N GLU C 248 " pdb=" C GLU C 248 " pdb=" CB GLU C 248 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.38e+00 chirality pdb=" CA GLU B 248 " pdb=" N GLU B 248 " pdb=" C GLU B 248 " pdb=" CB GLU B 248 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.37e+00 ... (remaining 933 not shown) Planarity restraints: 1131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 L9Q C 301 " 0.336 2.00e-02 2.50e+03 3.25e-01 1.06e+03 pdb=" C39 L9Q C 301 " -0.364 2.00e-02 2.50e+03 pdb=" C40 L9Q C 301 " -0.284 2.00e-02 2.50e+03 pdb=" C41 L9Q C 301 " 0.312 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q A 318 " 0.336 2.00e-02 2.50e+03 3.25e-01 1.06e+03 pdb=" C39 L9Q A 318 " -0.366 2.00e-02 2.50e+03 pdb=" C40 L9Q A 318 " -0.282 2.00e-02 2.50e+03 pdb=" C41 L9Q A 318 " 0.312 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q B 319 " -0.336 2.00e-02 2.50e+03 3.25e-01 1.06e+03 pdb=" C39 L9Q B 319 " 0.365 2.00e-02 2.50e+03 pdb=" C40 L9Q B 319 " 0.283 2.00e-02 2.50e+03 pdb=" C41 L9Q B 319 " -0.312 2.00e-02 2.50e+03 ... (remaining 1128 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.11: 30 2.11 - 2.81: 2166 2.81 - 3.51: 8981 3.51 - 4.20: 18754 4.20 - 4.90: 31681 Nonbonded interactions: 61612 Sorted by model distance: nonbonded pdb=" C40 L9Q A 319 " pdb=" C40 L9Q B 301 " model vdw 1.417 2.912 nonbonded pdb=" C40 L9Q B 301 " pdb=" C40 L9Q C 302 " model vdw 1.417 2.912 nonbonded pdb=" C45 L9Q B 301 " pdb=" C27 L9Q B 319 " model vdw 1.489 3.840 nonbonded pdb=" C27 L9Q A 318 " pdb=" C45 L9Q A 319 " model vdw 1.490 3.840 nonbonded pdb=" C27 L9Q C 301 " pdb=" C45 L9Q C 302 " model vdw 1.490 3.840 ... (remaining 61607 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 260 or resid 304 through 317)) selection = (chain 'B' and (resid 2 through 260 or resid 304 through 317)) selection = (chain 'C' and (resid 2 through 260 or resid 304 through 317)) } 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: 7.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.970 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.323 6906 Z= 1.286 Angle : 1.972 28.782 9330 Z= 1.024 Chirality : 0.136 0.579 936 Planarity : 0.021 0.325 1131 Dihedral : 27.728 175.942 2466 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.72 % Favored : 96.89 % Rotamer: Outliers : 16.44 % Allowed : 10.05 % Favored : 73.52 % Cbeta Deviations : 1.69 % 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: -2.87 (0.25), residues: 771 helix: -1.99 (0.17), residues: 525 sheet: None (None), residues: 0 loop : -1.22 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 244 TYR 0.024 0.003 TYR A 177 PHE 0.034 0.003 PHE B 165 TRP 0.021 0.004 TRP B 199 HIS 0.008 0.002 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.01664 / 1.12 ( 6900) covalent geometry : angle 1.97196 / 1.02 ( 9330) hydrogen bonds : bond 0.20747 / 14.17 ( 405) hydrogen bonds : angle 7.52770 / 5.31 ( 1206) Misc. bond : bond 0.21223 / 13.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 122 time to evaluate : 0.207 Fit side-chains REVERT: A 254 LEU cc_start: 0.8419 (mt) cc_final: 0.8194 (mp) REVERT: B 254 LEU cc_start: 0.8361 (mt) cc_final: 0.8127 (mp) REVERT: C 98 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: C 254 LEU cc_start: 0.8404 (mt) cc_final: 0.8202 (mp) outliers start: 108 outliers final: 17 residues processed: 194 average time/residue: 0.4015 time to fit residues: 82.9364 Evaluate side-chains 118 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 219 GLN C 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.129639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112941 restraints weight = 6235.938| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.24 r_work: 0.3169 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6906 Z= 0.154 Angle : 0.709 9.987 9330 Z= 0.337 Chirality : 0.041 0.154 936 Planarity : 0.007 0.049 1131 Dihedral : 26.769 144.152 1157 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 6.09 % Allowed : 14.16 % Favored : 79.76 % 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: 0.34 (0.29), residues: 771 helix: 0.64 (0.20), residues: 543 sheet: None (None), residues: 0 loop : -0.57 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 46 TYR 0.014 0.002 TYR C 180 PHE 0.017 0.002 PHE C 167 TRP 0.015 0.002 TRP B 42 HIS 0.003 0.001 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 6900) covalent geometry : angle 0.70895 / 0.34 ( 9330) hydrogen bonds : bond 0.04874 / 3.36 ( 405) hydrogen bonds : angle 4.62027 / 3.26 ( 1206) Misc. bond : bond 0.00353 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 0.239 Fit side-chains REVERT: A 9 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.5941 (pp20) REVERT: A 254 LEU cc_start: 0.8474 (mt) cc_final: 0.8269 (mp) REVERT: B 9 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.5905 (pp20) REVERT: C 9 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.5972 (pp20) REVERT: C 62 TYR cc_start: 0.8278 (m-80) cc_final: 0.7417 (m-80) REVERT: C 171 ARG cc_start: 0.7708 (mtm110) cc_final: 0.7327 (ttm110) REVERT: C 252 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7828 (mt-10) outliers start: 40 outliers final: 13 residues processed: 146 average time/residue: 0.3968 time to fit residues: 61.7336 Evaluate side-chains 112 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 28 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 59 optimal weight: 0.0570 chunk 24 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN A 125 HIS B 125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113730 restraints weight = 6208.816| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.17 r_work: 0.3181 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6906 Z= 0.124 Angle : 0.603 8.960 9330 Z= 0.280 Chirality : 0.039 0.119 936 Planarity : 0.006 0.043 1131 Dihedral : 22.487 140.775 1151 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 5.33 % Allowed : 13.85 % Favored : 80.82 % 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: 1.95 (0.31), residues: 771 helix: 2.01 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -0.21 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 46 TYR 0.010 0.001 TYR C 180 PHE 0.016 0.001 PHE C 167 TRP 0.011 0.001 TRP C 42 HIS 0.003 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6900) covalent geometry : angle 0.60298 / 0.28 ( 9330) hydrogen bonds : bond 0.04005 / 2.76 ( 405) hydrogen bonds : angle 4.21223 / 2.97 ( 1206) Misc. bond : bond 0.00241 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.244 Fit side-chains REVERT: A 9 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6195 (pp20) REVERT: B 9 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6130 (pp20) REVERT: B 68 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8349 (p) REVERT: B 238 LEU cc_start: 0.8288 (mt) cc_final: 0.8048 (mm) REVERT: C 9 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6103 (pp20) REVERT: C 171 ARG cc_start: 0.7481 (mtm110) cc_final: 0.7132 (ttm110) outliers start: 35 outliers final: 12 residues processed: 135 average time/residue: 0.3895 time to fit residues: 56.0234 Evaluate side-chains 113 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 145 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.125628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.109671 restraints weight = 6224.288| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.19 r_work: 0.3127 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6906 Z= 0.138 Angle : 0.625 7.802 9330 Z= 0.292 Chirality : 0.041 0.144 936 Planarity : 0.005 0.037 1131 Dihedral : 19.812 151.464 1148 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 5.18 % Allowed : 13.70 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.31), residues: 771 helix: 2.06 (0.22), residues: 543 sheet: None (None), residues: 0 loop : 0.02 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 171 TYR 0.013 0.002 TYR C 180 PHE 0.014 0.002 PHE B 167 TRP 0.011 0.001 TRP B 42 HIS 0.003 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6900) covalent geometry : angle 0.62542 / 0.29 ( 9330) hydrogen bonds : bond 0.04446 / 3.06 ( 405) hydrogen bonds : angle 4.22692 / 2.99 ( 1206) Misc. bond : bond 0.00227 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.262 Fit side-chains REVERT: A 9 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6277 (pp20) REVERT: A 252 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: B 9 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.6054 (pp20) REVERT: B 233 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8019 (mptt) REVERT: B 252 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: C 9 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.6029 (pp20) REVERT: C 28 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7693 (ttp) REVERT: C 171 ARG cc_start: 0.7481 (mtm110) cc_final: 0.7133 (ttm110) outliers start: 34 outliers final: 18 residues processed: 123 average time/residue: 0.4660 time to fit residues: 60.9320 Evaluate side-chains 117 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 9 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.121810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.106060 restraints weight = 6336.798| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.19 r_work: 0.3076 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6906 Z= 0.176 Angle : 0.668 7.798 9330 Z= 0.314 Chirality : 0.044 0.172 936 Planarity : 0.005 0.036 1131 Dihedral : 19.752 157.511 1148 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 5.78 % Allowed : 13.24 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.31), residues: 771 helix: 2.16 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -0.05 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 244 TYR 0.015 0.002 TYR A 177 PHE 0.012 0.002 PHE A 242 TRP 0.012 0.002 TRP C 42 HIS 0.003 0.001 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 6900) covalent geometry : angle 0.66787 / 0.31 ( 9330) hydrogen bonds : bond 0.04981 / 3.44 ( 405) hydrogen bonds : angle 4.35893 / 3.08 ( 1206) Misc. bond : bond 0.00270 / 0.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.247 Fit side-chains REVERT: A 4 CYS cc_start: 0.7399 (OUTLIER) cc_final: 0.6880 (t) REVERT: A 9 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6250 (pp20) REVERT: A 252 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: B 4 CYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6812 (t) REVERT: B 9 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6083 (pp20) REVERT: B 252 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: C 4 CYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7007 (t) REVERT: C 9 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.5980 (pp20) REVERT: C 171 ARG cc_start: 0.7544 (mtm110) cc_final: 0.7170 (ttm110) outliers start: 38 outliers final: 17 residues processed: 122 average time/residue: 0.4625 time to fit residues: 59.7373 Evaluate side-chains 115 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.124649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108999 restraints weight = 6292.215| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.19 r_work: 0.3118 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6906 Z= 0.129 Angle : 0.590 7.261 9330 Z= 0.276 Chirality : 0.040 0.156 936 Planarity : 0.005 0.035 1131 Dihedral : 19.015 161.924 1148 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 4.41 % Allowed : 14.76 % Favored : 80.82 % 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: 2.44 (0.31), residues: 771 helix: 2.19 (0.22), residues: 543 sheet: None (None), residues: 0 loop : 0.29 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 171 TYR 0.010 0.002 TYR B 22 PHE 0.013 0.001 PHE A 167 TRP 0.012 0.001 TRP B 42 HIS 0.002 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 6900) covalent geometry : angle 0.59040 / 0.28 ( 9330) hydrogen bonds : bond 0.04224 / 2.92 ( 405) hydrogen bonds : angle 4.18148 / 2.96 ( 1206) Misc. bond : bond 0.00213 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.240 Fit side-chains REVERT: A 4 CYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6883 (t) REVERT: A 252 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: B 4 CYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6762 (t) REVERT: B 9 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6113 (pp20) REVERT: C 4 CYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7020 (t) REVERT: C 9 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.5999 (pp20) REVERT: C 171 ARG cc_start: 0.7495 (mtm110) cc_final: 0.7150 (ttm110) outliers start: 29 outliers final: 16 residues processed: 121 average time/residue: 0.4911 time to fit residues: 63.0184 Evaluate side-chains 113 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 51 optimal weight: 0.0010 chunk 2 optimal weight: 0.5980 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.124181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.108636 restraints weight = 6211.523| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.18 r_work: 0.3096 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6906 Z= 0.158 Angle : 0.630 7.180 9330 Z= 0.297 Chirality : 0.043 0.169 936 Planarity : 0.005 0.035 1131 Dihedral : 18.839 166.055 1145 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 4.26 % Allowed : 14.76 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.31), residues: 771 helix: 2.25 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.10 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 171 TYR 0.013 0.002 TYR B 177 PHE 0.013 0.002 PHE A 167 TRP 0.013 0.002 TRP C 42 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 6900) covalent geometry : angle 0.63042 / 0.30 ( 9330) hydrogen bonds : bond 0.04702 / 3.24 ( 405) hydrogen bonds : angle 4.28692 / 3.03 ( 1206) Misc. bond : bond 0.00230 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.238 Fit side-chains REVERT: A 4 CYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7123 (t) REVERT: A 252 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: B 4 CYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7058 (t) REVERT: B 9 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6219 (pp20) REVERT: C 4 CYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7227 (t) REVERT: C 9 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6109 (pp20) REVERT: C 171 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7594 (ttm110) outliers start: 28 outliers final: 15 residues processed: 118 average time/residue: 0.4282 time to fit residues: 53.7029 Evaluate side-chains 113 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 171 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.124565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.108668 restraints weight = 6293.002| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.22 r_work: 0.3097 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6906 Z= 0.156 Angle : 0.616 6.936 9330 Z= 0.291 Chirality : 0.042 0.167 936 Planarity : 0.005 0.034 1131 Dihedral : 18.186 169.439 1145 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 4.11 % Allowed : 15.22 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.31), residues: 771 helix: 2.29 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.14 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 171 TYR 0.011 0.002 TYR B 177 PHE 0.013 0.002 PHE A 167 TRP 0.012 0.001 TRP B 42 HIS 0.002 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 6900) covalent geometry : angle 0.61637 / 0.29 ( 9330) hydrogen bonds : bond 0.04540 / 3.14 ( 405) hydrogen bonds : angle 4.25367 / 3.00 ( 1206) Misc. bond : bond 0.00228 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.252 Fit side-chains REVERT: A 4 CYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7073 (t) REVERT: A 252 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: B 4 CYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7061 (t) REVERT: B 9 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6229 (pp20) REVERT: C 4 CYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7205 (t) REVERT: C 9 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6116 (pp20) REVERT: C 171 ARG cc_start: 0.7865 (mtm110) cc_final: 0.7602 (ttm110) outliers start: 27 outliers final: 15 residues processed: 118 average time/residue: 0.4703 time to fit residues: 58.8919 Evaluate side-chains 112 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.121100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105252 restraints weight = 6283.997| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.21 r_work: 0.3052 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 6906 Z= 0.236 Angle : 0.717 7.331 9330 Z= 0.342 Chirality : 0.048 0.174 936 Planarity : 0.006 0.033 1131 Dihedral : 18.913 164.367 1145 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.50 % Allowed : 15.83 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.30), residues: 771 helix: 2.03 (0.21), residues: 522 sheet: None (None), residues: 0 loop : 0.04 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 171 TYR 0.019 0.003 TYR A 177 PHE 0.018 0.002 PHE B 3 TRP 0.012 0.002 TRP C 42 HIS 0.004 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.24 ( 6900) covalent geometry : angle 0.71663 / 0.34 ( 9330) hydrogen bonds : bond 0.05534 / 3.81 ( 405) hydrogen bonds : angle 4.44113 / 3.13 ( 1206) Misc. bond : bond 0.00294 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.301 Fit side-chains REVERT: A 4 CYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7183 (t) REVERT: A 252 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: B 4 CYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7126 (t) REVERT: B 9 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6192 (pp20) REVERT: C 4 CYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7244 (t) REVERT: C 9 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6085 (pp20) REVERT: C 171 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7696 (ttm110) outliers start: 23 outliers final: 14 residues processed: 109 average time/residue: 0.4645 time to fit residues: 53.6696 Evaluate side-chains 109 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 171 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 72 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 = 0.3421 r_free = 0.3421 target = 0.124950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.109102 restraints weight = 6196.621| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.21 r_work: 0.3105 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6906 Z= 0.142 Angle : 0.595 6.646 9330 Z= 0.283 Chirality : 0.041 0.154 936 Planarity : 0.005 0.035 1131 Dihedral : 18.084 168.104 1145 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.65 % Allowed : 15.83 % Favored : 80.52 % 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: 2.40 (0.30), residues: 771 helix: 2.28 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.15 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 171 TYR 0.012 0.002 TYR B 22 PHE 0.015 0.001 PHE A 167 TRP 0.013 0.001 TRP A 42 HIS 0.002 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 6900) covalent geometry : angle 0.59532 / 0.28 ( 9330) hydrogen bonds : bond 0.04409 / 3.05 ( 405) hydrogen bonds : angle 4.25248 / 3.01 ( 1206) Misc. bond : bond 0.00201 / 0.12 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.248 Fit side-chains REVERT: A 4 CYS cc_start: 0.7403 (OUTLIER) cc_final: 0.7056 (t) REVERT: A 252 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: B 4 CYS cc_start: 0.7345 (OUTLIER) cc_final: 0.7031 (t) REVERT: B 9 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6204 (pp20) REVERT: C 4 CYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7178 (t) REVERT: C 9 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6075 (pp20) REVERT: C 28 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7886 (ttp) REVERT: C 171 ARG cc_start: 0.7798 (mtm110) cc_final: 0.7533 (ttm110) outliers start: 24 outliers final: 14 residues processed: 114 average time/residue: 0.4826 time to fit residues: 58.4008 Evaluate side-chains 112 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.121035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105292 restraints weight = 6216.918| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.19 r_work: 0.3054 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6906 Z= 0.237 Angle : 0.711 6.891 9330 Z= 0.341 Chirality : 0.048 0.197 936 Planarity : 0.006 0.034 1131 Dihedral : 18.531 166.114 1145 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.65 % Allowed : 15.68 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.30), residues: 771 helix: 2.01 (0.21), residues: 522 sheet: None (None), residues: 0 loop : 0.10 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 171 TYR 0.019 0.003 TYR A 177 PHE 0.018 0.002 PHE B 3 TRP 0.013 0.002 TRP C 42 HIS 0.004 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.24 ( 6900) covalent geometry : angle 0.71058 / 0.34 ( 9330) hydrogen bonds : bond 0.05533 / 3.80 ( 405) hydrogen bonds : angle 4.45167 / 3.14 ( 1206) Misc. bond : bond 0.00282 / 0.16 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2413.44 seconds wall clock time: 42 minutes 0.26 seconds (2520.26 seconds total)