Starting phenix.real_space_refine on Tue Aug 4 22:29:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hhl_34803/08_2026/8hhl_34803.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhl_34803/08_2026/8hhl_34803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hhl_34803/08_2026/8hhl_34803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhl_34803/08_2026/8hhl_34803.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hhl_34803/08_2026/8hhl_34803.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hhl_34803/08_2026/8hhl_34803.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hhl_34803/08_2026/8hhl_34803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhl_34803/08_2026/8hhl_34803.map" } resolution = 2.87 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 ------------------------------------------------------------------------------- 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= -0.012 sd= 0.253 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 111 5.49 5 Mg 3 5.21 5 S 19 5.16 5 C 3939 2.51 5 N 1321 2.21 5 O 1577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6971 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1066 Classifications: {'RNAv2': 49} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 28, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 43} Chain: "C" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 624 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 647 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "A" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4630 Classifications: {'peptide': 592} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 567} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6663 SG CYS A 552 87.861 24.922 31.530 1.00120.60 S ATOM 6796 SG CYS A 569 84.715 23.574 29.746 1.00120.99 S ATOM 6814 SG CYS A 572 86.921 21.084 31.118 1.00121.86 S Time building chain proxies: 1.34, per 1000 atoms: 0.19 Number of scatterers: 6971 At special positions: 0 Unit cell: (101.094, 89.474, 103.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 19 16.00 P 111 15.00 Mg 3 11.99 O 1577 8.00 N 1321 7.00 C 3939 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: 0.50 Conformation dependent library (CDL) restraints added in 288.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 549 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 572 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 552 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 569 " Number of angles added : 3 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 58.1% alpha, 14.4% beta 40 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 18 through 52 Processing helix chain 'A' and resid 53 through 85 Processing helix chain 'A' and resid 90 through 118 removed outlier: 3.558A pdb=" N THR A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 145 Processing helix chain 'A' and resid 151 through 176 Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.605A pdb=" N LEU A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 362 through 397 removed outlier: 4.195A pdb=" N GLU A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 417 through 428 removed outlier: 4.230A pdb=" N PHE A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 434 through 479 removed outlier: 3.520A pdb=" N TRP A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 500 removed outlier: 4.495A pdb=" N MET A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLU A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 518 through 534 Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.570A pdb=" N LEU A 563 " --> pdb=" O ASP A 560 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 564 " --> pdb=" O ARG A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 564' Processing helix chain 'A' and resid 579 through 591 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195 removed outlier: 6.076A pdb=" N ILE A 278 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG A 301 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 280 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA A 294 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 10 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY A 253 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE A 262 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG A 251 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A 264 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG A 249 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 266 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THR A 247 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 360 removed outlier: 4.813A pdb=" N THR A 327 " --> pdb=" O ARG A 321 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG A 321 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 329 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 485 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A 318 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 567 through 568 300 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1580 1.33 - 1.45: 2077 1.45 - 1.57: 3432 1.57 - 1.69: 219 1.69 - 1.81: 31 Bond restraints: 7339 Sorted by residual: bond pdb=" C3' DG D -9 " pdb=" O3' DG D -9 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" C5' DT D -8 " pdb=" C4' DT D -8 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 9.88e+00 bond pdb=" C5' DG D -9 " pdb=" C4' DG D -9 " ideal model delta sigma weight residual 1.512 1.533 -0.021 7.00e-03 2.04e+04 9.21e+00 bond pdb=" C1' DT D -8 " pdb=" N1 DT D -8 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 8.89e+00 bond pdb=" C3' DC C 0 " pdb=" C2' DC C 0 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.60e+00 ... (remaining 7334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 9760 1.18 - 2.36: 496 2.36 - 3.55: 186 3.55 - 4.73: 19 4.73 - 5.91: 9 Bond angle restraints: 10470 Sorted by residual: angle pdb=" N3 DT D -8 " pdb=" C4 DT D -8 " pdb=" O4 DT D -8 " ideal model delta sigma weight residual 119.90 122.76 -2.86 6.00e-01 2.78e+00 2.27e+01 angle pdb=" O4' DT D 5 " pdb=" C4' DT D 5 " pdb=" C3' DT D 5 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT C 13 " pdb=" C4 DT C 13 " pdb=" O4 DT C 13 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" O4 DT D -8 " pdb=" C4 DT D -8 " pdb=" C5 DT D -8 " ideal model delta sigma weight residual 124.90 121.85 3.05 7.00e-01 2.04e+00 1.90e+01 angle pdb=" N3 DT C 15 " pdb=" C4 DT C 15 " pdb=" O4 DT C 15 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 10465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.75: 3498 23.75 - 47.50: 443 47.50 - 71.25: 173 71.25 - 95.00: 10 95.00 - 118.75: 1 Dihedral angle restraints: 4125 sinusoidal: 2402 harmonic: 1723 Sorted by residual: dihedral pdb=" C4' G B 1 " pdb=" C3' G B 1 " pdb=" C2' G B 1 " pdb=" C1' G B 1 " ideal model delta sinusoidal sigma weight residual 36.34 -37.12 73.46 1 3.10e+00 1.04e-01 7.15e+02 dihedral pdb=" C4' A B -23 " pdb=" C3' A B -23 " pdb=" C2' A B -23 " pdb=" C1' A B -23 " ideal model delta sinusoidal sigma weight residual 36.34 -35.92 72.26 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" C4' G B -11 " pdb=" C3' G B -11 " pdb=" C2' G B -11 " pdb=" C1' G B -11 " ideal model delta sinusoidal sigma weight residual 36.35 -35.81 72.16 1 3.10e+00 1.04e-01 6.93e+02 ... (remaining 4122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 995 0.060 - 0.120: 141 0.120 - 0.180: 17 0.180 - 0.239: 44 0.239 - 0.299: 13 Chirality restraints: 1210 Sorted by residual: chirality pdb=" C3' G B 1 " pdb=" C4' G B 1 " pdb=" O3' G B 1 " pdb=" C2' G B 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C2' C B -12 " pdb=" C3' C B -12 " pdb=" O2' C B -12 " pdb=" C1' C B -12 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C2' G B -8 " pdb=" C3' G B -8 " pdb=" O2' G B -8 " pdb=" C1' G B -8 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 1207 not shown) Planarity restraints: 951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG D 0 " 0.027 2.00e-02 2.50e+03 1.15e-02 3.97e+00 pdb=" N9 DG D 0 " -0.028 2.00e-02 2.50e+03 pdb=" C8 DG D 0 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG D 0 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG D 0 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG D 0 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG D 0 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG D 0 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG D 0 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG D 0 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG D 0 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG D 0 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 2 " 0.025 2.00e-02 2.50e+03 1.06e-02 3.34e+00 pdb=" N9 G B 2 " -0.024 2.00e-02 2.50e+03 pdb=" C8 G B 2 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G B 2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 2 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B 2 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G B 2 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G B 2 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 2 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 2 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 2 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G B 2 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 452 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C GLN A 452 " -0.031 2.00e-02 2.50e+03 pdb=" O GLN A 452 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 453 " 0.010 2.00e-02 2.50e+03 ... (remaining 948 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 215 2.68 - 3.24: 6117 3.24 - 3.79: 12497 3.79 - 4.35: 16282 4.35 - 4.90: 24625 Nonbonded interactions: 59736 Sorted by model distance: nonbonded pdb=" OD1 ASP A 579 " pdb="MG MG A 601 " model vdw 2.126 2.170 nonbonded pdb=" OP1 G B -22 " pdb="MG MG B 101 " model vdw 2.134 2.170 nonbonded pdb=" OP1 DG D 15 " pdb="MG MG A 601 " model vdw 2.143 2.170 nonbonded pdb=" OG SER A 334 " pdb=" O ALA A 336 " model vdw 2.154 3.040 nonbonded pdb=" NE2 HIS A 317 " pdb="MG MG A 601 " model vdw 2.198 2.250 ... (remaining 59731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.810 Find NCS groups from input model: 0.030 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:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 7343 Z= 0.365 Angle : 0.679 9.011 10473 Z= 0.470 Chirality : 0.064 0.299 1210 Planarity : 0.004 0.042 951 Dihedral : 21.105 118.750 3005 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.29 % Allowed : 12.29 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.35), residues: 590 helix: 2.63 (0.29), residues: 323 sheet: 1.62 (0.63), residues: 60 loop : -0.37 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 185 TYR 0.010 0.001 TYR A 42 PHE 0.006 0.001 PHE A 443 TRP 0.008 0.001 TRP A 232 HIS 0.002 0.000 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.36 ( 7339) covalent geometry : angle 0.66774 / 0.47 (10470) hydrogen bonds : bond 0.12160 / 6.11 ( 405) hydrogen bonds : angle 5.09844 / 2.14 ( 1085) metal coordination : bond 0.03038 / 1.52 ( 4) metal coordination : angle 7.17526 / 2.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.200 Fit side-chains REVERT: A 63 MET cc_start: 0.8112 (ttt) cc_final: 0.7844 (ttp) REVERT: A 160 ASP cc_start: 0.7952 (m-30) cc_final: 0.7678 (m-30) REVERT: A 172 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7002 (mm-40) REVERT: A 199 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7586 (tt0) REVERT: A 264 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8790 (mt) REVERT: A 404 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7712 (p0) REVERT: A 416 LYS cc_start: 0.6723 (mttt) cc_final: 0.5308 (tttm) REVERT: A 458 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7645 (mmm-85) REVERT: A 575 MET cc_start: 0.8659 (mtp) cc_final: 0.8283 (mtt) outliers start: 11 outliers final: 2 residues processed: 82 average time/residue: 0.6015 time to fit residues: 51.3103 Evaluate side-chains 51 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 404 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 95 GLN A 242 GLN A 478 GLN A 556 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.137725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105535 restraints weight = 9766.389| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.49 r_work: 0.3212 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7343 Z= 0.217 Angle : 0.860 17.477 10473 Z= 0.419 Chirality : 0.076 1.421 1210 Planarity : 0.006 0.101 951 Dihedral : 21.966 129.050 1923 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.54 % Allowed : 17.08 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.34), residues: 590 helix: 3.00 (0.28), residues: 323 sheet: 1.91 (0.62), residues: 60 loop : -0.31 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 85 TYR 0.010 0.001 TYR A 42 PHE 0.006 0.001 PHE A 155 TRP 0.012 0.001 TRP A 232 HIS 0.003 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.22 ( 7339) covalent geometry : angle 0.85957 / 0.42 (10470) hydrogen bonds : bond 0.05249 / 2.73 ( 405) hydrogen bonds : angle 3.69611 / 1.58 ( 1085) metal coordination : bond 0.00285 / 0.14 ( 4) metal coordination : angle 1.32102 / 0.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.177 Fit side-chains REVERT: A 63 MET cc_start: 0.8298 (ttt) cc_final: 0.8026 (ttp) REVERT: A 85 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.8097 (tpp80) REVERT: A 89 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8170 (pp) REVERT: A 160 ASP cc_start: 0.8158 (m-30) cc_final: 0.7949 (m-30) REVERT: A 172 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7410 (mm-40) REVERT: A 264 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9070 (mt) REVERT: A 325 GLU cc_start: 0.8285 (mp0) cc_final: 0.8071 (mp0) REVERT: A 416 LYS cc_start: 0.6796 (mttt) cc_final: 0.5485 (tttm) REVERT: A 458 ARG cc_start: 0.8765 (mmm160) cc_final: 0.8257 (mmm-85) REVERT: A 459 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.8041 (mttp) REVERT: A 575 MET cc_start: 0.8611 (mtp) cc_final: 0.8220 (mtt) outliers start: 17 outliers final: 7 residues processed: 63 average time/residue: 0.5891 time to fit residues: 38.6366 Evaluate side-chains 56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 0.0570 chunk 7 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 0.6980 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107938 restraints weight = 9760.899| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.51 r_work: 0.3262 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7343 Z= 0.152 Angle : 0.713 12.284 10473 Z= 0.355 Chirality : 0.058 0.896 1210 Planarity : 0.004 0.061 951 Dihedral : 22.054 140.587 1921 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 4.17 % Allowed : 18.33 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.34), residues: 590 helix: 3.21 (0.28), residues: 324 sheet: 1.84 (0.62), residues: 60 loop : -0.13 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 185 TYR 0.008 0.001 TYR A 42 PHE 0.005 0.001 PHE A 155 TRP 0.009 0.001 TRP A 232 HIS 0.001 0.000 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 ( 7339) covalent geometry : angle 0.71249 / 0.35 (10470) hydrogen bonds : bond 0.04560 / 2.40 ( 405) hydrogen bonds : angle 3.43152 / 1.45 ( 1085) metal coordination : bond 0.00158 / 0.08 ( 4) metal coordination : angle 0.79028 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.117 Fit side-chains REVERT: A 63 MET cc_start: 0.8273 (ttt) cc_final: 0.7979 (ttp) REVERT: A 88 LYS cc_start: 0.8390 (tppt) cc_final: 0.7907 (mmmt) REVERT: A 89 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7930 (pp) REVERT: A 146 ARG cc_start: 0.8678 (mtp85) cc_final: 0.8108 (mtm-85) REVERT: A 172 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7356 (mm-40) REVERT: A 416 LYS cc_start: 0.6707 (mttt) cc_final: 0.5439 (tttm) REVERT: A 458 ARG cc_start: 0.8738 (mmm160) cc_final: 0.8355 (mmm-85) REVERT: A 498 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: A 575 MET cc_start: 0.8607 (mtp) cc_final: 0.8234 (mtt) outliers start: 20 outliers final: 5 residues processed: 62 average time/residue: 0.6245 time to fit residues: 40.2557 Evaluate side-chains 51 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.0170 chunk 29 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 478 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.140883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108973 restraints weight = 9809.096| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.51 r_work: 0.3287 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7343 Z= 0.139 Angle : 0.675 10.110 10473 Z= 0.339 Chirality : 0.053 0.619 1210 Planarity : 0.004 0.043 951 Dihedral : 21.944 137.655 1918 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 4.38 % Allowed : 16.88 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.34), residues: 590 helix: 3.32 (0.28), residues: 324 sheet: 1.63 (0.61), residues: 62 loop : -0.05 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 85 TYR 0.007 0.001 TYR A 42 PHE 0.004 0.001 PHE A 155 TRP 0.009 0.001 TRP A 232 HIS 0.001 0.000 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 ( 7339) covalent geometry : angle 0.67493 / 0.34 (10470) hydrogen bonds : bond 0.04245 / 2.23 ( 405) hydrogen bonds : angle 3.25327 / 1.38 ( 1085) metal coordination : bond 0.00082 / 0.04 ( 4) metal coordination : angle 0.60666 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.149 Fit side-chains REVERT: A 63 MET cc_start: 0.8240 (ttt) cc_final: 0.7897 (ttp) REVERT: A 89 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8005 (pp) REVERT: A 98 ARG cc_start: 0.8046 (mtp-110) cc_final: 0.7521 (mtm110) REVERT: A 103 ARG cc_start: 0.8025 (mtm180) cc_final: 0.7797 (mtm180) REVERT: A 146 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8111 (mtm-85) REVERT: A 160 ASP cc_start: 0.7959 (m-30) cc_final: 0.7754 (m-30) REVERT: A 172 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7309 (mm-40) REVERT: A 335 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8703 (t0) REVERT: A 416 LYS cc_start: 0.6596 (mttt) cc_final: 0.5387 (tttm) REVERT: A 458 ARG cc_start: 0.8758 (mmm160) cc_final: 0.8393 (mmm-85) REVERT: A 498 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6383 (mp0) REVERT: A 575 MET cc_start: 0.8590 (mtp) cc_final: 0.8194 (mtt) REVERT: A 580 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8036 (mtm110) outliers start: 21 outliers final: 9 residues processed: 60 average time/residue: 0.5963 time to fit residues: 37.2964 Evaluate side-chains 56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 580 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 21 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 27 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.8135 > 50:) chunk 4 optimal weight: 50.0000 chunk 64 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.137524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.105339 restraints weight = 9830.347| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.51 r_work: 0.3218 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7343 Z= 0.222 Angle : 0.726 10.314 10473 Z= 0.363 Chirality : 0.057 0.693 1210 Planarity : 0.005 0.069 951 Dihedral : 22.008 134.810 1918 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.33 % Allowed : 19.58 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.34), residues: 590 helix: 3.18 (0.27), residues: 324 sheet: 1.48 (0.60), residues: 62 loop : -0.20 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 547 TYR 0.009 0.001 TYR A 42 PHE 0.008 0.002 PHE A 443 TRP 0.009 0.001 TRP A 232 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.22 ( 7339) covalent geometry : angle 0.72589 / 0.36 (10470) hydrogen bonds : bond 0.04906 / 2.56 ( 405) hydrogen bonds : angle 3.43939 / 1.44 ( 1085) metal coordination : bond 0.00303 / 0.15 ( 4) metal coordination : angle 0.80433 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.193 Fit side-chains REVERT: A 63 MET cc_start: 0.8304 (ttt) cc_final: 0.8005 (ttp) REVERT: A 89 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8237 (pp) REVERT: A 98 ARG cc_start: 0.8176 (mtp-110) cc_final: 0.7816 (mtm-85) REVERT: A 160 ASP cc_start: 0.8060 (m-30) cc_final: 0.7832 (m-30) REVERT: A 172 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7480 (mm-40) REVERT: A 367 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7800 (ttp-110) REVERT: A 416 LYS cc_start: 0.6642 (mttt) cc_final: 0.5336 (tttm) REVERT: A 458 ARG cc_start: 0.8763 (mmm160) cc_final: 0.8350 (mmm-85) REVERT: A 498 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6444 (mp0) REVERT: A 575 MET cc_start: 0.8611 (mtp) cc_final: 0.8221 (mtt) REVERT: A 580 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7948 (mtm110) outliers start: 16 outliers final: 8 residues processed: 57 average time/residue: 0.6732 time to fit residues: 39.8130 Evaluate side-chains 56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 580 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 9 optimal weight: 40.0000 chunk 51 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.103448 restraints weight = 9867.704| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.50 r_work: 0.3191 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 : 0.005 0.049 7343 Z= 0.251 Angle : 0.757 10.148 10473 Z= 0.378 Chirality : 0.059 0.709 1210 Planarity : 0.005 0.069 951 Dihedral : 22.136 134.037 1918 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.79 % Allowed : 18.33 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.33), residues: 590 helix: 2.96 (0.27), residues: 324 sheet: 1.41 (0.60), residues: 62 loop : -0.34 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 85 TYR 0.010 0.002 TYR A 42 PHE 0.008 0.002 PHE A 443 TRP 0.010 0.002 TRP A 232 HIS 0.003 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.25 ( 7339) covalent geometry : angle 0.75655 / 0.38 (10470) hydrogen bonds : bond 0.05236 / 2.74 ( 405) hydrogen bonds : angle 3.59324 / 1.51 ( 1085) metal coordination : bond 0.00417 / 0.21 ( 4) metal coordination : angle 0.75989 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.158 Fit side-chains REVERT: A 63 MET cc_start: 0.8297 (ttt) cc_final: 0.7993 (ttp) REVERT: A 89 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8173 (pp) REVERT: A 98 ARG cc_start: 0.8209 (mtp-110) cc_final: 0.7865 (mtm-85) REVERT: A 160 ASP cc_start: 0.8034 (m-30) cc_final: 0.7796 (m-30) REVERT: A 172 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7512 (mm-40) REVERT: A 335 ASP cc_start: 0.9066 (OUTLIER) cc_final: 0.8797 (t0) REVERT: A 367 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7868 (ttp-110) REVERT: A 416 LYS cc_start: 0.6725 (mttt) cc_final: 0.5361 (tttm) REVERT: A 458 ARG cc_start: 0.8782 (mmm160) cc_final: 0.8386 (mmm-85) REVERT: A 498 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6355 (pm20) REVERT: A 575 MET cc_start: 0.8590 (mtp) cc_final: 0.8201 (mtt) outliers start: 23 outliers final: 13 residues processed: 64 average time/residue: 0.5912 time to fit residues: 39.4223 Evaluate side-chains 64 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105299 restraints weight = 9734.840| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.43 r_work: 0.3248 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7343 Z= 0.154 Angle : 0.686 8.416 10473 Z= 0.346 Chirality : 0.052 0.547 1210 Planarity : 0.004 0.057 951 Dihedral : 22.089 138.084 1918 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.33 % Allowed : 20.00 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.34), residues: 590 helix: 3.28 (0.27), residues: 324 sheet: 1.35 (0.59), residues: 62 loop : -0.27 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.009 0.001 TYR A 42 PHE 0.005 0.001 PHE A 155 TRP 0.011 0.001 TRP A 232 HIS 0.002 0.000 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 ( 7339) covalent geometry : angle 0.68624 / 0.35 (10470) hydrogen bonds : bond 0.04490 / 2.36 ( 405) hydrogen bonds : angle 3.34783 / 1.43 ( 1085) metal coordination : bond 0.00140 / 0.07 ( 4) metal coordination : angle 0.61098 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.205 Fit side-chains REVERT: A 63 MET cc_start: 0.8268 (ttt) cc_final: 0.7976 (ttp) REVERT: A 89 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8325 (pp) REVERT: A 98 ARG cc_start: 0.8172 (mtp-110) cc_final: 0.7597 (mtm110) REVERT: A 160 ASP cc_start: 0.8054 (m-30) cc_final: 0.7826 (m-30) REVERT: A 172 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7392 (mm-40) REVERT: A 367 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7837 (ttp-110) REVERT: A 413 LYS cc_start: 0.8107 (tttt) cc_final: 0.7083 (tptp) REVERT: A 416 LYS cc_start: 0.6608 (mttt) cc_final: 0.5314 (tttm) REVERT: A 458 ARG cc_start: 0.8777 (mmm160) cc_final: 0.8389 (mmm-85) REVERT: A 498 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: A 575 MET cc_start: 0.8581 (mtp) cc_final: 0.8191 (mtt) outliers start: 16 outliers final: 8 residues processed: 59 average time/residue: 0.7792 time to fit residues: 47.7016 Evaluate side-chains 57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 50 optimal weight: 0.0670 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 overall best weight: 2.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.137737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105438 restraints weight = 9839.906| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.48 r_work: 0.3239 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7343 Z= 0.170 Angle : 0.692 8.798 10473 Z= 0.347 Chirality : 0.053 0.560 1210 Planarity : 0.004 0.051 951 Dihedral : 22.051 136.015 1918 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.50 % Allowed : 21.25 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.34), residues: 590 helix: 3.28 (0.27), residues: 324 sheet: 1.34 (0.60), residues: 62 loop : -0.28 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 580 TYR 0.008 0.001 TYR A 42 PHE 0.006 0.001 PHE A 443 TRP 0.010 0.001 TRP A 232 HIS 0.002 0.000 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 ( 7339) covalent geometry : angle 0.69182 / 0.35 (10470) hydrogen bonds : bond 0.04574 / 2.40 ( 405) hydrogen bonds : angle 3.34350 / 1.42 ( 1085) metal coordination : bond 0.00210 / 0.10 ( 4) metal coordination : angle 0.59110 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.209 Fit side-chains REVERT: A 63 MET cc_start: 0.8272 (ttt) cc_final: 0.8004 (ttp) REVERT: A 89 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8130 (pp) REVERT: A 98 ARG cc_start: 0.8171 (mtp-110) cc_final: 0.7896 (mtm-85) REVERT: A 160 ASP cc_start: 0.8086 (m-30) cc_final: 0.7848 (m-30) REVERT: A 172 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7421 (mm-40) REVERT: A 348 MET cc_start: 0.9126 (ttt) cc_final: 0.8919 (ttt) REVERT: A 367 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7846 (ttp-110) REVERT: A 413 LYS cc_start: 0.8117 (tttt) cc_final: 0.7118 (tptp) REVERT: A 416 LYS cc_start: 0.6617 (mttt) cc_final: 0.5319 (tttm) REVERT: A 458 ARG cc_start: 0.8783 (mmm160) cc_final: 0.8390 (mmm-85) REVERT: A 498 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: A 575 MET cc_start: 0.8584 (mtp) cc_final: 0.8195 (mtt) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.7877 time to fit residues: 46.6945 Evaluate side-chains 58 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.137257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105087 restraints weight = 9827.443| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.48 r_work: 0.3237 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7343 Z= 0.169 Angle : 0.691 8.605 10473 Z= 0.348 Chirality : 0.053 0.546 1210 Planarity : 0.004 0.051 951 Dihedral : 22.053 136.137 1918 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.12 % Allowed : 20.83 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.34), residues: 590 helix: 3.29 (0.27), residues: 324 sheet: 1.34 (0.59), residues: 62 loop : -0.26 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.008 0.001 TYR A 42 PHE 0.006 0.001 PHE A 443 TRP 0.010 0.001 TRP A 232 HIS 0.002 0.000 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 ( 7339) covalent geometry : angle 0.69121 / 0.35 (10470) hydrogen bonds : bond 0.04543 / 2.38 ( 405) hydrogen bonds : angle 3.32463 / 1.41 ( 1085) metal coordination : bond 0.00192 / 0.10 ( 4) metal coordination : angle 0.59055 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.198 Fit side-chains REVERT: A 63 MET cc_start: 0.8266 (ttt) cc_final: 0.7984 (ttp) REVERT: A 89 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8398 (pp) REVERT: A 98 ARG cc_start: 0.8170 (mtp-110) cc_final: 0.7636 (mtm110) REVERT: A 160 ASP cc_start: 0.8082 (m-30) cc_final: 0.7841 (m-30) REVERT: A 172 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7407 (mm-40) REVERT: A 367 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7827 (ttp-110) REVERT: A 413 LYS cc_start: 0.8111 (tttt) cc_final: 0.7119 (tptp) REVERT: A 416 LYS cc_start: 0.6616 (mttt) cc_final: 0.5314 (tttm) REVERT: A 458 ARG cc_start: 0.8789 (mmm160) cc_final: 0.8386 (mmm-85) REVERT: A 498 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6375 (mp0) REVERT: A 575 MET cc_start: 0.8585 (mtp) cc_final: 0.8207 (mtt) outliers start: 15 outliers final: 9 residues processed: 58 average time/residue: 0.7064 time to fit residues: 42.6591 Evaluate side-chains 58 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 61 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 30.0000 chunk 65 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.107545 restraints weight = 9695.547| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.47 r_work: 0.3277 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7343 Z= 0.143 Angle : 0.674 8.480 10473 Z= 0.340 Chirality : 0.051 0.503 1210 Planarity : 0.004 0.051 951 Dihedral : 22.017 137.256 1918 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.08 % Allowed : 21.67 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.34), residues: 590 helix: 3.43 (0.27), residues: 324 sheet: 1.39 (0.59), residues: 62 loop : -0.21 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.007 0.001 TYR A 42 PHE 0.005 0.001 PHE A 155 TRP 0.011 0.001 TRP A 232 HIS 0.002 0.000 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 ( 7339) covalent geometry : angle 0.67406 / 0.34 (10470) hydrogen bonds : bond 0.04241 / 2.22 ( 405) hydrogen bonds : angle 3.21692 / 1.38 ( 1085) metal coordination : bond 0.00099 / 0.05 ( 4) metal coordination : angle 0.48609 / 0.16 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.162 Fit side-chains REVERT: A 63 MET cc_start: 0.8242 (ttt) cc_final: 0.7953 (ttp) REVERT: A 98 ARG cc_start: 0.8148 (mtp-110) cc_final: 0.7660 (mtm110) REVERT: A 160 ASP cc_start: 0.8017 (m-30) cc_final: 0.7779 (m-30) REVERT: A 172 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7351 (mm-40) REVERT: A 335 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8770 (t0) REVERT: A 367 ARG cc_start: 0.8044 (mtp85) cc_final: 0.7763 (ttp-110) REVERT: A 413 LYS cc_start: 0.8057 (tttt) cc_final: 0.7065 (tptp) REVERT: A 416 LYS cc_start: 0.6572 (mttt) cc_final: 0.5292 (tttm) REVERT: A 458 ARG cc_start: 0.8762 (mmm160) cc_final: 0.8328 (mmm-85) REVERT: A 498 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6450 (mp0) REVERT: A 575 MET cc_start: 0.8587 (mtp) cc_final: 0.8198 (mtt) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 0.7361 time to fit residues: 40.5839 Evaluate side-chains 55 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 560 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 47 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 9 optimal weight: 40.0000 chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.141502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109469 restraints weight = 9767.526| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.50 r_work: 0.3301 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7343 Z= 0.136 Angle : 0.668 10.470 10473 Z= 0.335 Chirality : 0.050 0.495 1210 Planarity : 0.004 0.049 951 Dihedral : 21.953 137.022 1918 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.29 % Allowed : 21.67 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.34), residues: 590 helix: 3.44 (0.27), residues: 324 sheet: 1.44 (0.58), residues: 62 loop : -0.20 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 499 TYR 0.007 0.001 TYR A 42 PHE 0.005 0.001 PHE A 155 TRP 0.012 0.001 TRP A 232 HIS 0.002 0.000 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 ( 7339) covalent geometry : angle 0.66847 / 0.34 (10470) hydrogen bonds : bond 0.04089 / 2.14 ( 405) hydrogen bonds : angle 3.17495 / 1.36 ( 1085) metal coordination : bond 0.00083 / 0.04 ( 4) metal coordination : angle 0.37262 / 0.12 ( 3) =============================================================================== Job complete usr+sys time: 2032.92 seconds wall clock time: 35 minutes 14.76 seconds (2114.76 seconds total)