Starting phenix.real_space_refine on Fri Aug 22 18:06:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ifu_35423/08_2025/8ifu_35423_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifu_35423/08_2025/8ifu_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_35423/08_2025/8ifu_35423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifu_35423/08_2025/8ifu_35423.map" model { file = "/net/cci-nas-00/data/ceres_data/8ifu_35423/08_2025/8ifu_35423_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifu_35423/08_2025/8ifu_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 138 Unusual residues: {' NA': 16, 'L9Q': 2, 'RET': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} 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, 138 Unusual residues: {' NA': 16, 'L9Q': 2, 'RET': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} 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, 138 Unusual residues: {' NA': 16, 'L9Q': 2, 'RET': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} 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: 2.21, per 1000 atoms: 0.33 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: 0.78 Conformation dependent library (CDL) restraints added in 395.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.21 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: 1.13 Time building geometry restraints manager: 0.97 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: 9.670 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.370 Find NCS groups from input model: 0.160 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:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 aren 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 covalent geometry : bond 0.01664 ( 6900) covalent geometry : angle 1.97196 ( 9330) hydrogen bonds : bond 0.20747 ( 405) hydrogen bonds : angle 7.52770 ( 1206) Misc. bond : bond 0.21223 ( 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 : 0.256 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: 0.4658 time to fit residues: 96.0628 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 : 0.292 ------------------------------------------------------------------------------- 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: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3475 r_free = 0.3475 target = 0.129053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.112408 restraints weight = 6252.184| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.23 r_work: 0.3156 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2502 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= 0.152 Angle : 0.717 9.142 9330 Z= 0.338 Chirality : 0.042 0.156 936 Planarity : 0.007 0.050 1131 Dihedral : 27.082 145.883 1157 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 6.39 % Allowed : 14.16 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.29), residues: 771 helix: 0.73 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.49 (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 0.018 0.002 PHE A 167 TRP 0.015 0.001 TRP B 42 HIS 0.002 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6900) covalent geometry : angle 0.71698 ( 9330) hydrogen bonds : bond 0.04845 ( 405) hydrogen bonds : angle 4.62957 ( 1206) Misc. bond : bond 0.00381 ( 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: 42 poor density : 108 time to evaluate : 0.251 Fit side-chains REVERT: A 9 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.5947 (pp20) REVERT: A 254 LEU cc_start: 0.8494 (mt) cc_final: 0.8291 (mp) REVERT: B 9 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.5882 (pp20) REVERT: C 9 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.5948 (pp20) REVERT: C 62 TYR cc_start: 0.8264 (m-80) cc_final: 0.7389 (m-80) REVERT: C 171 ARG cc_start: 0.7730 (mtm110) cc_final: 0.7355 (ttm110) REVERT: C 252 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7866 (mt-10) outliers start: 42 outliers final: 16 residues processed: 146 average time/residue: 0.4815 time to fit residues: 74.6201 Evaluate side-chains 116 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 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 68 SER 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 234 THR 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: 3.9990 chunk 11 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN B 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.126461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.110697 restraints weight = 6229.945| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.17 r_work: 0.3136 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3089 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= 0.137 Angle : 0.632 8.848 9330 Z= 0.294 Chirality : 0.040 0.132 936 Planarity : 0.006 0.045 1131 Dihedral : 22.982 137.824 1152 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 5.63 % Allowed : 13.55 % 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 aren not related in a simple way. whole: 1.74 (0.31), residues: 771 helix: 1.71 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.12 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 46 TYR 0.012 0.002 TYR C 180 PHE 0.018 0.002 PHE A 167 TRP 0.012 0.001 TRP C 42 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6900) covalent geometry : angle 0.63206 ( 9330) hydrogen bonds : bond 0.04387 ( 405) hydrogen bonds : angle 4.27741 ( 1206) Misc. bond : bond 0.00247 ( 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 137 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.254 Fit side-chains REVERT: A 9 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6168 (pp20) REVERT: B 9 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6086 (pp20) REVERT: C 9 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.5998 (pp20) REVERT: C 28 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7682 (ttp) REVERT: C 171 ARG cc_start: 0.7518 (mtm110) cc_final: 0.7165 (ttm110) REVERT: C 252 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7805 (mt-10) outliers start: 37 outliers final: 15 residues processed: 129 average time/residue: 0.4842 time to fit residues: 66.2005 Evaluate side-chains 112 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 160 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 28 MET Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 64 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.109707 restraints weight = 6253.447| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.18 r_work: 0.3121 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3340 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= 0.133 Angle : 0.624 7.942 9330 Z= 0.287 Chirality : 0.041 0.152 936 Planarity : 0.005 0.037 1131 Dihedral : 20.338 150.593 1149 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 5.48 % Allowed : 12.94 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.31), residues: 771 helix: 2.06 (0.22), residues: 543 sheet: None (None), residues: 0 loop : 0.07 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 244 TYR 0.012 0.002 TYR A 180 PHE 0.013 0.001 PHE B 167 TRP 0.011 0.001 TRP A 42 HIS 0.003 0.001 HIS B 172 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6900) covalent geometry : angle 0.62374 ( 9330) hydrogen bonds : bond 0.04302 ( 405) hydrogen bonds : angle 4.24338 ( 1206) Misc. bond : bond 0.00259 ( 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 136 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.242 Fit side-chains REVERT: A 9 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6301 (pp20) REVERT: A 252 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: B 9 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6055 (pp20) REVERT: C 9 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6015 (pp20) REVERT: C 28 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7741 (ttp) REVERT: C 171 ARG cc_start: 0.7551 (mtm110) cc_final: 0.7209 (ttm110) REVERT: C 252 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7800 (mt-10) outliers start: 36 outliers final: 19 residues processed: 129 average time/residue: 0.5429 time to fit residues: 73.9664 Evaluate side-chains 122 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 201 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 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 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.108334 restraints weight = 6363.210| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.19 r_work: 0.3103 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3424 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= 0.140 Angle : 0.614 7.444 9330 Z= 0.286 Chirality : 0.041 0.164 936 Planarity : 0.005 0.036 1131 Dihedral : 19.578 156.400 1149 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 5.18 % Allowed : 13.55 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.31), residues: 771 helix: 2.36 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.13 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 244 TYR 0.011 0.002 TYR A 180 PHE 0.012 0.001 PHE A 167 TRP 0.012 0.001 TRP C 42 HIS 0.002 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6900) covalent geometry : angle 0.61375 ( 9330) hydrogen bonds : bond 0.04413 ( 405) hydrogen bonds : angle 4.24591 ( 1206) Misc. bond : bond 0.00270 ( 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 136 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.249 Fit side-chains REVERT: A 4 CYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6892 (t) REVERT: A 9 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6273 (pp20) REVERT: A 252 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: B 4 CYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6808 (t) REVERT: B 9 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6106 (pp20) REVERT: B 252 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: C 4 CYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6960 (t) REVERT: C 9 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5980 (pp20) REVERT: C 28 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7726 (ttp) REVERT: C 171 ARG cc_start: 0.7511 (mtm110) cc_final: 0.7165 (ttm110) REVERT: C 252 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7529 (mt-10) outliers start: 34 outliers final: 18 residues processed: 131 average time/residue: 0.4952 time to fit residues: 68.7307 Evaluate side-chains 123 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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 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 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 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.109036 restraints weight = 6301.700| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.18 r_work: 0.3111 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3533 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= 0.130 Angle : 0.590 6.931 9330 Z= 0.276 Chirality : 0.040 0.151 936 Planarity : 0.005 0.035 1131 Dihedral : 19.149 163.678 1149 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 5.18 % Allowed : 13.85 % 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 aren not related in a simple way. whole: 2.64 (0.31), residues: 771 helix: 2.45 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.27 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 46 TYR 0.010 0.002 TYR B 177 PHE 0.011 0.001 PHE A 167 TRP 0.012 0.001 TRP A 42 HIS 0.002 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6900) covalent geometry : angle 0.58954 ( 9330) hydrogen bonds : bond 0.04203 ( 405) hydrogen bonds : angle 4.17702 ( 1206) Misc. bond : bond 0.00260 ( 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 135 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.255 Fit side-chains REVERT: A 4 CYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6895 (t) REVERT: A 252 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: B 4 CYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6814 (t) REVERT: B 9 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6132 (pp20) REVERT: B 252 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: C 4 CYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7022 (t) REVERT: C 9 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5999 (pp20) REVERT: C 28 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7700 (ttp) REVERT: C 171 ARG cc_start: 0.7515 (mtm110) cc_final: 0.7181 (ttm110) REVERT: C 252 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7503 (mt-10) outliers start: 34 outliers final: 19 residues processed: 128 average time/residue: 0.5184 time to fit residues: 70.3500 Evaluate side-chains 123 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 3 PHE Chi-restraints excluded: chain B residue 4 CYS 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 201 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 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 234 THR Chi-restraints excluded: chain C residue 252 GLU 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: 0.7980 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 chunk 2 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.111633 restraints weight = 6218.444| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.20 r_work: 0.3136 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3688 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= 0.122 Angle : 0.570 6.586 9330 Z= 0.268 Chirality : 0.040 0.138 936 Planarity : 0.005 0.034 1131 Dihedral : 18.213 171.640 1146 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 4.87 % Allowed : 14.00 % 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 aren not related in a simple way. whole: 2.78 (0.31), residues: 771 helix: 2.56 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.32 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 151 TYR 0.009 0.001 TYR A 180 PHE 0.011 0.001 PHE A 167 TRP 0.012 0.001 TRP A 42 HIS 0.002 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6900) covalent geometry : angle 0.57030 ( 9330) hydrogen bonds : bond 0.04025 ( 405) hydrogen bonds : angle 4.13501 ( 1206) Misc. bond : bond 0.00258 ( 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 135 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.266 Fit side-chains REVERT: A 4 CYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7062 (t) REVERT: A 25 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8053 (mp) REVERT: A 252 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: B 4 CYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6969 (t) REVERT: B 9 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6208 (pp20) REVERT: C 4 CYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7156 (t) REVERT: C 9 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6151 (pp20) REVERT: C 28 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7957 (ttp) REVERT: C 171 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7516 (ttm110) REVERT: C 252 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7587 (mt-10) outliers start: 32 outliers final: 16 residues processed: 130 average time/residue: 0.4880 time to fit residues: 67.3760 Evaluate side-chains 121 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS 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 4 CYS 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 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 Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 252 GLU 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: 0.2980 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.108766 restraints weight = 6322.269| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.19 r_work: 0.3097 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6906 Z= 0.154 Angle : 0.614 6.500 9330 Z= 0.291 Chirality : 0.042 0.157 936 Planarity : 0.005 0.034 1131 Dihedral : 18.210 172.812 1146 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 4.57 % Allowed : 14.16 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.31), residues: 771 helix: 2.38 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.30 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 171 TYR 0.012 0.002 TYR B 177 PHE 0.012 0.002 PHE A 167 TRP 0.012 0.001 TRP A 42 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6900) covalent geometry : angle 0.61361 ( 9330) hydrogen bonds : bond 0.04551 ( 405) hydrogen bonds : angle 4.25515 ( 1206) Misc. bond : bond 0.00286 ( 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 130 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.287 Fit side-chains REVERT: A 4 CYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7099 (t) REVERT: A 252 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: B 4 CYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7091 (t) REVERT: B 9 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6231 (pp20) REVERT: C 4 CYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7228 (t) REVERT: C 9 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6145 (pp20) REVERT: C 28 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7928 (ttp) REVERT: C 171 ARG cc_start: 0.7870 (mtm110) cc_final: 0.7543 (ttm110) REVERT: C 252 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7625 (mt-10) outliers start: 30 outliers final: 17 residues processed: 127 average time/residue: 0.4951 time to fit residues: 66.7209 Evaluate side-chains 123 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104502 restraints weight = 6324.278| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.19 r_work: 0.3040 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 6906 Z= 0.270 Angle : 0.759 7.431 9330 Z= 0.362 Chirality : 0.051 0.200 936 Planarity : 0.006 0.033 1131 Dihedral : 19.318 167.083 1146 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.11 % Allowed : 14.61 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.30), residues: 771 helix: 2.00 (0.21), residues: 519 sheet: None (None), residues: 0 loop : 0.13 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 171 TYR 0.022 0.003 TYR A 177 PHE 0.021 0.003 PHE A 3 TRP 0.012 0.002 TRP A 42 HIS 0.005 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00654 ( 6900) covalent geometry : angle 0.75859 ( 9330) hydrogen bonds : bond 0.05853 ( 405) hydrogen bonds : angle 4.51877 ( 1206) Misc. bond : bond 0.00430 ( 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 123 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.258 Fit side-chains REVERT: A 4 CYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7169 (t) REVERT: A 252 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: B 4 CYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7188 (t) REVERT: B 9 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6200 (pp20) REVERT: C 4 CYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7276 (t) REVERT: C 9 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6080 (pp20) REVERT: C 252 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7882 (mt-10) outliers start: 27 outliers final: 15 residues processed: 118 average time/residue: 0.5159 time to fit residues: 64.5717 Evaluate side-chains 110 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.109075 restraints weight = 6281.728| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.19 r_work: 0.3098 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3688 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= 0.134 Angle : 0.586 6.595 9330 Z= 0.278 Chirality : 0.041 0.162 936 Planarity : 0.005 0.034 1131 Dihedral : 18.287 169.191 1146 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 3.50 % Allowed : 15.22 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.30), residues: 771 helix: 2.32 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.30 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 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 C 172 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6900) covalent geometry : angle 0.58610 ( 9330) hydrogen bonds : bond 0.04265 ( 405) hydrogen bonds : angle 4.25690 ( 1206) Misc. bond : bond 0.00271 ( 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 119 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.267 Fit side-chains REVERT: A 4 CYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7094 (t) REVERT: A 252 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: B 4 CYS cc_start: 0.7331 (OUTLIER) cc_final: 0.7082 (t) REVERT: B 9 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6201 (pp20) REVERT: C 4 CYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7204 (t) REVERT: C 9 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6108 (pp20) REVERT: C 171 ARG cc_start: 0.7783 (mtm110) cc_final: 0.7501 (ttm110) REVERT: C 252 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7870 (mt-10) outliers start: 23 outliers final: 14 residues processed: 118 average time/residue: 0.5526 time to fit residues: 68.8936 Evaluate side-chains 114 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 0.0670 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.108395 restraints weight = 6270.882| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.19 r_work: 0.3094 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6906 Z= 0.142 Angle : 0.590 6.187 9330 Z= 0.282 Chirality : 0.041 0.161 936 Planarity : 0.005 0.034 1131 Dihedral : 18.018 166.308 1146 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.20 % Allowed : 15.53 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.30), residues: 771 helix: 2.35 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.37 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 171 TYR 0.011 0.002 TYR B 22 PHE 0.014 0.001 PHE A 167 TRP 0.013 0.001 TRP A 42 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6900) covalent geometry : angle 0.58993 ( 9330) hydrogen bonds : bond 0.04425 ( 405) hydrogen bonds : angle 4.24748 ( 1206) Misc. bond : bond 0.00275 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2838.99 seconds wall clock time: 49 minutes 25.06 seconds (2965.06 seconds total)