Starting phenix.real_space_refine on Thu Jul 2 05:50:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqj_62506/07_2026/9kqj_62506.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqj_62506/07_2026/9kqj_62506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kqj_62506/07_2026/9kqj_62506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqj_62506/07_2026/9kqj_62506.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kqj_62506/07_2026/9kqj_62506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqj_62506/07_2026/9kqj_62506.map" } resolution = 2.95 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= 0.002 sd= 0.093 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 Ca 2 9.91 5 P 16 5.49 5 S 40 5.16 5 C 4818 2.51 5 N 1016 2.21 5 O 1164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7056 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3171 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 364} Chain breaks: 1 Chain: "B" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3171 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 364} Chain breaks: 1 Chain: "A" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 356 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'C14': 1, 'D12': 1, 'LBN': 5, 'PSF': 2, 'T7X': 1} Classifications: {'undetermined': 10} Link IDs: {None: 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'LBN:plan-3': 2} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 356 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'C14': 1, 'D12': 1, 'LBN': 5, 'PSF': 2, 'T7X': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'LBN:plan-3': 2} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 1.81, per 1000 atoms: 0.26 Number of scatterers: 7056 At special positions: 0 Unit cell: (94.95, 108.665, 71.74, 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) Ca 2 19.99 S 40 16.00 P 16 15.00 O 1164 8.00 N 1016 7.00 C 4818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 334.4 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1436 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 77.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.559A pdb=" N LYS A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.598A pdb=" N PHE A 37 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 39 " --> pdb=" O PHE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 59 Processing helix chain 'A' and resid 64 through 88 Processing helix chain 'A' and resid 97 through 119 removed outlier: 4.017A pdb=" N TRP A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 185 through 203 Processing helix chain 'A' and resid 213 through 220 removed outlier: 4.316A pdb=" N GLN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 283 through 311 removed outlier: 3.619A pdb=" N LYS A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 344 removed outlier: 3.785A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 351 through 372 Processing helix chain 'A' and resid 381 through 408 removed outlier: 3.677A pdb=" N VAL A 391 " --> pdb=" O TRP A 387 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 394 " --> pdb=" O CYS A 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 25 removed outlier: 3.611A pdb=" N MET B 23 " --> pdb=" O MET B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 59 Processing helix chain 'B' and resid 64 through 88 removed outlier: 3.533A pdb=" N ILE B 69 " --> pdb=" O PRO B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 119 removed outlier: 4.066A pdb=" N TRP B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 134 removed outlier: 3.523A pdb=" N ASP B 134 " --> pdb=" O MET B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 166 through 184 removed outlier: 3.548A pdb=" N GLY B 171 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 182 " --> pdb=" O MET B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 203 removed outlier: 3.860A pdb=" N GLU B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 219 removed outlier: 4.453A pdb=" N GLN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'B' and resid 255 through 265 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 283 through 311 removed outlier: 3.717A pdb=" N GLN B 298 " --> pdb=" O MET B 294 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 301 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B 302 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS B 309 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 344 removed outlier: 3.831A pdb=" N ARG B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 3.654A pdb=" N ARG B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 372 removed outlier: 3.847A pdb=" N ALA B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 408 removed outlier: 3.513A pdb=" N LEU B 389 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 391 " --> pdb=" O TRP B 387 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 394 " --> pdb=" O CYS B 390 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 976 1.32 - 1.44: 2253 1.44 - 1.56: 3941 1.56 - 1.69: 32 1.69 - 1.81: 62 Bond restraints: 7264 Sorted by residual: bond pdb=" CG1 ILE A 192 " pdb=" CD1 ILE A 192 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.56e+00 bond pdb=" CG1 ILE B 192 " pdb=" CD1 ILE B 192 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.32e+00 bond pdb=" CB GLN B 298 " pdb=" CG GLN B 298 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CG1 ILE B 50 " pdb=" CD1 ILE B 50 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.37e-01 bond pdb=" CG LEU B 46 " pdb=" CD2 LEU B 46 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.65e-01 ... (remaining 7259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 9629 2.11 - 4.23: 115 4.23 - 6.34: 21 6.34 - 8.45: 3 8.45 - 10.56: 2 Bond angle restraints: 9770 Sorted by residual: angle pdb=" C VAL A 218 " pdb=" N ILE A 219 " pdb=" CA ILE A 219 " ideal model delta sigma weight residual 122.97 119.36 3.61 9.80e-01 1.04e+00 1.35e+01 angle pdb=" CA LEU A 386 " pdb=" CB LEU A 386 " pdb=" CG LEU A 386 " ideal model delta sigma weight residual 116.30 126.86 -10.56 3.50e+00 8.16e-02 9.11e+00 angle pdb=" CA LEU B 386 " pdb=" CB LEU B 386 " pdb=" CG LEU B 386 " ideal model delta sigma weight residual 116.30 125.89 -9.59 3.50e+00 8.16e-02 7.51e+00 angle pdb=" CA MET A 19 " pdb=" CB MET A 19 " pdb=" CG MET A 19 " ideal model delta sigma weight residual 114.10 119.50 -5.40 2.00e+00 2.50e-01 7.29e+00 angle pdb=" CB MET A 19 " pdb=" CG MET A 19 " pdb=" SD MET A 19 " ideal model delta sigma weight residual 112.70 120.39 -7.69 3.00e+00 1.11e-01 6.56e+00 ... (remaining 9765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 3966 35.64 - 71.29: 219 71.29 - 106.93: 28 106.93 - 142.58: 14 142.58 - 178.22: 13 Dihedral angle restraints: 4240 sinusoidal: 2022 harmonic: 2218 Sorted by residual: dihedral pdb=" C1 LBN B 509 " pdb=" O1 LBN B 509 " pdb=" P1 LBN B 509 " pdb=" O3 LBN B 509 " ideal model delta sinusoidal sigma weight residual -84.60 93.62 -178.22 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN A 507 " pdb=" O1 LBN A 507 " pdb=" P1 LBN A 507 " pdb=" O3 LBN A 507 " ideal model delta sinusoidal sigma weight residual -84.60 93.51 -178.11 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN A 503 " pdb=" C2 LBN A 503 " pdb=" C3 LBN A 503 " pdb=" O7 LBN A 503 " ideal model delta sinusoidal sigma weight residual 62.67 -105.21 167.88 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 4237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 658 0.038 - 0.076: 270 0.076 - 0.113: 59 0.113 - 0.151: 11 0.151 - 0.189: 4 Chirality restraints: 1002 Sorted by residual: chirality pdb=" C4 T7X B 501 " pdb=" C3 T7X B 501 " pdb=" C5 T7X B 501 " pdb=" O4 T7X B 501 " both_signs ideal model delta sigma weight residual False -2.52 -2.33 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" C4 T7X A 510 " pdb=" C3 T7X A 510 " pdb=" C5 T7X A 510 " pdb=" O4 T7X A 510 " both_signs ideal model delta sigma weight residual False -2.52 -2.33 -0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" C1 T7X B 501 " pdb=" C2 T7X B 501 " pdb=" C6 T7X B 501 " pdb=" O1 T7X B 501 " both_signs ideal model delta sigma weight residual False -2.42 -2.25 -0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 999 not shown) Planarity restraints: 1126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 36 " 0.010 2.00e-02 2.50e+03 1.42e-02 3.51e+00 pdb=" CG PHE B 36 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 36 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 36 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 36 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 36 " -0.009 2.00e-02 2.50e+03 1.42e-02 3.51e+00 pdb=" CG PHE A 36 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 36 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 36 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 36 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 317 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO B 318 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 318 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 318 " 0.021 5.00e-02 4.00e+02 ... (remaining 1123 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 128 2.66 - 3.22: 6339 3.22 - 3.78: 10714 3.78 - 4.34: 15572 4.34 - 4.90: 25677 Nonbonded interactions: 58430 Sorted by model distance: nonbonded pdb=" O TYR B 55 " pdb=" OG1 THR B 59 " model vdw 2.099 3.040 nonbonded pdb=" O TYR A 55 " pdb=" OG1 THR A 59 " model vdw 2.102 3.040 nonbonded pdb=" O HIS B 246 " pdb=" ND1 HIS B 246 " model vdw 2.121 3.120 nonbonded pdb=" O HIS A 246 " pdb=" ND1 HIS A 246 " model vdw 2.129 3.120 nonbonded pdb=" O GLY B 289 " pdb=" OH TYR B 338 " model vdw 2.178 3.040 ... (remaining 58425 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 14 through 408) selection = (chain 'B' and resid 14 through 408) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.760 Find NCS groups from input model: 0.120 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:8.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7264 Z= 0.201 Angle : 0.623 10.563 9770 Z= 0.298 Chirality : 0.043 0.189 1002 Planarity : 0.004 0.037 1126 Dihedral : 24.654 178.222 2804 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.24 % Allowed : 20.65 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.91 (0.30), residues: 746 helix: -0.45 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.59 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 22 TYR 0.015 0.001 TYR A 17 PHE 0.032 0.002 PHE B 36 TRP 0.013 0.001 TRP A 321 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.20 ( 7264) covalent geometry : angle 0.62347 / 0.30 ( 9770) hydrogen bonds : bond 0.22037 / 14.12 ( 405) hydrogen bonds : angle 8.26990 / 6.20 ( 1200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.235 Fit side-chains outliers start: 22 outliers final: 22 residues processed: 92 average time/residue: 0.6150 time to fit residues: 59.2950 Evaluate side-chains 92 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 395 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS A 125 GLN A 205 HIS A 346 GLN B 41 HIS B 125 GLN B 205 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.164453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133799 restraints weight = 7301.720| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.69 r_work: 0.3475 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7264 Z= 0.141 Angle : 0.598 8.404 9770 Z= 0.287 Chirality : 0.043 0.212 1002 Planarity : 0.004 0.033 1126 Dihedral : 25.335 178.613 1432 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.98 % Allowed : 18.88 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.44 (0.30), residues: 746 helix: 0.73 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.71 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 22 TYR 0.011 0.001 TYR A 17 PHE 0.018 0.001 PHE B 36 TRP 0.015 0.001 TRP A 321 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 7264) covalent geometry : angle 0.59784 / 0.29 ( 9770) hydrogen bonds : bond 0.04320 / 2.83 ( 405) hydrogen bonds : angle 4.94534 / 3.59 ( 1200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.314 Fit side-chains REVERT: A 22 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.7351 (ttm-80) REVERT: A 162 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7590 (pp) REVERT: A 170 PHE cc_start: 0.6585 (OUTLIER) cc_final: 0.6048 (t80) REVERT: A 393 PHE cc_start: 0.6422 (t80) cc_final: 0.5791 (t80) REVERT: B 22 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.7235 (ttm-80) REVERT: B 162 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7700 (pp) REVERT: B 308 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7510 (ttpp) outliers start: 27 outliers final: 8 residues processed: 86 average time/residue: 0.5685 time to fit residues: 51.5831 Evaluate side-chains 72 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 402 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.168910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138791 restraints weight = 7183.514| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.68 r_work: 0.3481 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7264 Z= 0.143 Angle : 0.572 9.106 9770 Z= 0.271 Chirality : 0.043 0.218 1002 Planarity : 0.004 0.029 1126 Dihedral : 24.388 179.229 1402 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.83 % Allowed : 18.88 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.91 (0.30), residues: 746 helix: 1.13 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.75 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 22 TYR 0.010 0.001 TYR A 17 PHE 0.012 0.001 PHE B 21 TRP 0.016 0.001 TRP B 321 HIS 0.003 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 7264) covalent geometry : angle 0.57210 / 0.27 ( 9770) hydrogen bonds : bond 0.04031 / 2.63 ( 405) hydrogen bonds : angle 4.65916 / 3.37 ( 1200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.203 Fit side-chains REVERT: A 22 ARG cc_start: 0.7549 (ttm-80) cc_final: 0.7298 (ttm-80) REVERT: A 170 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.6042 (t80) REVERT: A 204 MET cc_start: 0.6673 (pp-130) cc_final: 0.6234 (ppp) REVERT: A 309 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7431 (m90) REVERT: B 22 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7148 (ttm-80) REVERT: B 245 TYR cc_start: 0.8141 (m-80) cc_final: 0.7932 (m-80) REVERT: B 308 LYS cc_start: 0.7916 (ttmt) cc_final: 0.7194 (ttpt) outliers start: 26 outliers final: 8 residues processed: 84 average time/residue: 0.6586 time to fit residues: 58.1942 Evaluate side-chains 70 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 384 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 37 optimal weight: 0.0970 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.168789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138624 restraints weight = 7221.401| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.68 r_work: 0.3481 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7264 Z= 0.146 Angle : 0.563 8.639 9770 Z= 0.268 Chirality : 0.043 0.234 1002 Planarity : 0.004 0.029 1126 Dihedral : 23.637 179.587 1400 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.10 % Allowed : 19.76 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.12 (0.30), residues: 746 helix: 1.30 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.74 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.010 0.001 TYR A 17 PHE 0.019 0.001 PHE B 36 TRP 0.016 0.001 TRP B 321 HIS 0.003 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 7264) covalent geometry : angle 0.56321 / 0.27 ( 9770) hydrogen bonds : bond 0.03868 / 2.54 ( 405) hydrogen bonds : angle 4.53776 / 3.28 ( 1200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.211 Fit side-chains REVERT: A 22 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.7275 (ttm-80) REVERT: A 170 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.6173 (t80) REVERT: A 309 HIS cc_start: 0.8039 (OUTLIER) cc_final: 0.7477 (m90) REVERT: A 346 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7524 (mm110) REVERT: A 393 PHE cc_start: 0.6461 (t80) cc_final: 0.5921 (t80) REVERT: B 308 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7189 (ttpt) outliers start: 21 outliers final: 9 residues processed: 78 average time/residue: 0.5916 time to fit residues: 48.6593 Evaluate side-chains 73 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 384 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.167038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136649 restraints weight = 7286.027| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.68 r_work: 0.3459 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7264 Z= 0.182 Angle : 0.603 9.696 9770 Z= 0.287 Chirality : 0.045 0.238 1002 Planarity : 0.004 0.030 1126 Dihedral : 23.682 178.270 1397 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.39 % Allowed : 19.32 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.08 (0.30), residues: 746 helix: 1.28 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.76 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.011 0.001 TYR A 17 PHE 0.012 0.001 PHE B 21 TRP 0.016 0.002 TRP B 321 HIS 0.003 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 ( 7264) covalent geometry : angle 0.60306 / 0.29 ( 9770) hydrogen bonds : bond 0.04150 / 2.73 ( 405) hydrogen bonds : angle 4.56895 / 3.31 ( 1200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 162 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7631 (pp) REVERT: A 278 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7706 (m-80) REVERT: A 309 HIS cc_start: 0.8044 (OUTLIER) cc_final: 0.7435 (m90) REVERT: A 346 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7541 (mm110) REVERT: A 393 PHE cc_start: 0.6497 (t80) cc_final: 0.5899 (t80) REVERT: B 204 MET cc_start: 0.6738 (pp-130) cc_final: 0.6350 (pp-130) REVERT: B 308 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7060 (ttpt) outliers start: 23 outliers final: 14 residues processed: 80 average time/residue: 0.6246 time to fit residues: 52.6291 Evaluate side-chains 78 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 278 PHE Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.167641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137380 restraints weight = 7284.185| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.69 r_work: 0.3494 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7264 Z= 0.129 Angle : 0.551 10.128 9770 Z= 0.262 Chirality : 0.042 0.225 1002 Planarity : 0.003 0.029 1126 Dihedral : 23.161 179.771 1397 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.24 % Allowed : 20.21 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.33 (0.30), residues: 746 helix: 1.49 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.78 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 22 TYR 0.010 0.001 TYR A 17 PHE 0.025 0.001 PHE B 36 TRP 0.017 0.001 TRP B 321 HIS 0.003 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 7264) covalent geometry : angle 0.55089 / 0.26 ( 9770) hydrogen bonds : bond 0.03659 / 2.40 ( 405) hydrogen bonds : angle 4.40430 / 3.18 ( 1200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.262 Fit side-chains REVERT: A 22 ARG cc_start: 0.7581 (ttm-80) cc_final: 0.7169 (ttm-80) REVERT: A 170 PHE cc_start: 0.6580 (OUTLIER) cc_final: 0.5939 (t80) REVERT: A 309 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7474 (m90) REVERT: A 393 PHE cc_start: 0.6492 (t80) cc_final: 0.5916 (t80) REVERT: B 308 LYS cc_start: 0.7755 (ttmt) cc_final: 0.7056 (ttpt) REVERT: B 399 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6092 (mp) outliers start: 22 outliers final: 13 residues processed: 80 average time/residue: 0.5687 time to fit residues: 47.7990 Evaluate side-chains 73 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.166587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136989 restraints weight = 7271.826| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.60 r_work: 0.3296 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7264 Z= 0.204 Angle : 0.635 10.580 9770 Z= 0.301 Chirality : 0.046 0.238 1002 Planarity : 0.004 0.032 1126 Dihedral : 23.635 178.939 1397 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.98 % Allowed : 19.91 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.09 (0.30), residues: 746 helix: 1.30 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.78 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 22 TYR 0.016 0.001 TYR A 186 PHE 0.011 0.001 PHE A 293 TRP 0.015 0.002 TRP B 321 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.20 ( 7264) covalent geometry : angle 0.63528 / 0.30 ( 9770) hydrogen bonds : bond 0.04259 / 2.80 ( 405) hydrogen bonds : angle 4.55270 / 3.30 ( 1200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7501 (ttm-80) cc_final: 0.7134 (ttm-80) REVERT: A 162 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7627 (pp) REVERT: A 184 ARG cc_start: 0.7667 (tpt170) cc_final: 0.7358 (tmt-80) REVERT: A 309 HIS cc_start: 0.8044 (OUTLIER) cc_final: 0.7461 (m90) REVERT: A 346 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7479 (mm110) REVERT: A 393 PHE cc_start: 0.6404 (t80) cc_final: 0.5797 (t80) REVERT: B 162 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7448 (pp) REVERT: B 308 LYS cc_start: 0.7688 (ttmt) cc_final: 0.6941 (ttpt) REVERT: B 399 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.5866 (mp) outliers start: 27 outliers final: 15 residues processed: 79 average time/residue: 0.5305 time to fit residues: 44.3578 Evaluate side-chains 77 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.168142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137795 restraints weight = 7346.460| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.70 r_work: 0.3474 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7264 Z= 0.159 Angle : 0.592 10.879 9770 Z= 0.280 Chirality : 0.044 0.221 1002 Planarity : 0.004 0.030 1126 Dihedral : 23.383 179.819 1397 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.54 % Allowed : 20.94 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.21 (0.30), residues: 746 helix: 1.40 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.80 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 22 TYR 0.013 0.001 TYR A 186 PHE 0.028 0.001 PHE B 36 TRP 0.017 0.001 TRP B 321 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 7264) covalent geometry : angle 0.59187 / 0.28 ( 9770) hydrogen bonds : bond 0.03941 / 2.59 ( 405) hydrogen bonds : angle 4.47007 / 3.23 ( 1200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.241 Fit side-chains REVERT: A 22 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.7200 (ttm-80) REVERT: A 162 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7535 (pp) REVERT: A 170 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.6195 (t80) REVERT: A 184 ARG cc_start: 0.7627 (tpt170) cc_final: 0.7337 (tmt-80) REVERT: A 309 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7426 (m90) REVERT: A 346 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7521 (mm110) REVERT: A 393 PHE cc_start: 0.6506 (t80) cc_final: 0.5915 (t80) REVERT: A 399 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.5891 (mp) REVERT: B 308 LYS cc_start: 0.7866 (ttmt) cc_final: 0.7053 (ttpt) REVERT: B 399 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.5926 (mp) outliers start: 24 outliers final: 14 residues processed: 77 average time/residue: 0.5693 time to fit residues: 46.2175 Evaluate side-chains 78 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.169960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.139935 restraints weight = 7247.664| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.68 r_work: 0.3499 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7264 Z= 0.126 Angle : 0.560 11.299 9770 Z= 0.264 Chirality : 0.042 0.209 1002 Planarity : 0.003 0.030 1126 Dihedral : 22.842 178.208 1397 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.65 % Allowed : 22.27 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.42 (0.30), residues: 746 helix: 1.57 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.80 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 22 TYR 0.012 0.001 TYR A 186 PHE 0.009 0.001 PHE A 79 TRP 0.019 0.001 TRP B 321 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7264) covalent geometry : angle 0.55958 / 0.26 ( 9770) hydrogen bonds : bond 0.03613 / 2.37 ( 405) hydrogen bonds : angle 4.35446 / 3.14 ( 1200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.260 Fit side-chains REVERT: A 22 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.7152 (ttm-80) REVERT: A 170 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.5928 (t80) REVERT: A 242 MET cc_start: 0.7760 (mmm) cc_final: 0.7540 (mtt) REVERT: A 309 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7436 (m90) REVERT: A 346 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7493 (mm110) REVERT: A 393 PHE cc_start: 0.6484 (t80) cc_final: 0.5909 (t80) REVERT: A 399 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.5922 (mp) REVERT: B 308 LYS cc_start: 0.7758 (ttmt) cc_final: 0.7144 (ttpp) REVERT: B 399 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.5783 (mp) outliers start: 18 outliers final: 12 residues processed: 67 average time/residue: 0.5994 time to fit residues: 42.4020 Evaluate side-chains 69 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 5 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 71 optimal weight: 0.0050 chunk 19 optimal weight: 3.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.169855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139861 restraints weight = 7247.924| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.67 r_work: 0.3498 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7264 Z= 0.130 Angle : 0.577 11.428 9770 Z= 0.271 Chirality : 0.043 0.211 1002 Planarity : 0.003 0.029 1126 Dihedral : 22.732 178.089 1396 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.65 % Allowed : 21.98 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.44 (0.30), residues: 746 helix: 1.60 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.81 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 22 TYR 0.012 0.001 TYR A 186 PHE 0.010 0.001 PHE B 37 TRP 0.019 0.001 TRP B 321 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7264) covalent geometry : angle 0.57715 / 0.27 ( 9770) hydrogen bonds : bond 0.03666 / 2.41 ( 405) hydrogen bonds : angle 4.34575 / 3.14 ( 1200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.240 Fit side-chains REVERT: A 22 ARG cc_start: 0.7540 (ttm-80) cc_final: 0.7134 (ttm-80) REVERT: A 170 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.5930 (t80) REVERT: A 184 ARG cc_start: 0.7581 (tpt170) cc_final: 0.7232 (tmt-80) REVERT: A 242 MET cc_start: 0.7789 (mmm) cc_final: 0.7566 (mtt) REVERT: A 309 HIS cc_start: 0.7921 (OUTLIER) cc_final: 0.7402 (m90) REVERT: A 346 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7508 (mm110) REVERT: A 393 PHE cc_start: 0.6345 (t80) cc_final: 0.5803 (t80) REVERT: A 399 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.5953 (mp) REVERT: B 36 PHE cc_start: 0.7985 (t80) cc_final: 0.7780 (t80) REVERT: B 308 LYS cc_start: 0.7774 (ttmt) cc_final: 0.7152 (ttpp) REVERT: B 399 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.5912 (mp) outliers start: 18 outliers final: 12 residues processed: 66 average time/residue: 0.4944 time to fit residues: 34.6107 Evaluate side-chains 70 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.170030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139927 restraints weight = 7258.108| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.68 r_work: 0.3493 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7264 Z= 0.130 Angle : 0.573 11.350 9770 Z= 0.269 Chirality : 0.043 0.212 1002 Planarity : 0.003 0.029 1126 Dihedral : 22.507 179.772 1396 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.80 % Allowed : 21.83 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.46 (0.30), residues: 746 helix: 1.61 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.81 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 22 TYR 0.012 0.001 TYR A 186 PHE 0.009 0.001 PHE A 278 TRP 0.019 0.001 TRP B 321 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 7264) covalent geometry : angle 0.57343 / 0.27 ( 9770) hydrogen bonds : bond 0.03653 / 2.40 ( 405) hydrogen bonds : angle 4.32762 / 3.12 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2172.67 seconds wall clock time: 37 minutes 50.87 seconds (2270.87 seconds total)