Starting phenix.real_space_refine on Thu Jul 2 06:19:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hhl_34803/07_2026/8hhl_34803.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhl_34803/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8hhl_34803/07_2026/8hhl_34803.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hhl_34803/07_2026/8hhl_34803.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hhl_34803/07_2026/8hhl_34803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhl_34803/07_2026/8hhl_34803.map" model { file = "/net/cci-nas-00/data/ceres_data/8hhl_34803/07_2026/8hhl_34803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhl_34803/07_2026/8hhl_34803.cif" } 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-dev-6108/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: {'RNA': 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: 1.51, per 1000 atoms: 0.22 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: 0.45 Conformation dependent library (CDL) restraints added in 264.9 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: 0.76 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: 0.97 Time building geometry restraints manager: 0.58 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: 9910 1.18 - 2.36: 453 2.36 - 3.55: 95 3.55 - 4.73: 9 4.73 - 5.91: 3 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: 3565 23.75 - 47.50: 403 47.50 - 71.25: 149 71.25 - 95.00: 7 95.00 - 118.75: 1 Dihedral angle restraints: 4125 sinusoidal: 2402 harmonic: 1723 Sorted by residual: dihedral pdb=" O4' G B -11 " pdb=" C1' G B -11 " pdb=" N9 G B -11 " pdb=" C4 G B -11 " ideal model delta sinusoidal sigma weight residual -106.00 -172.34 66.34 1 1.70e+01 3.46e-03 1.99e+01 dihedral pdb=" C4' DG D -9 " pdb=" C3' DG D -9 " pdb=" O3' DG D -9 " pdb=" P DT D -8 " ideal model delta sinusoidal sigma weight residual 220.00 101.25 118.75 1 3.50e+01 8.16e-04 1.16e+01 dihedral pdb=" CA ASP A 477 " pdb=" CB ASP A 477 " pdb=" CG ASP A 477 " pdb=" OD1 ASP A 477 " ideal model delta sinusoidal sigma weight residual -30.00 -86.97 56.97 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 4122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 862 0.036 - 0.071: 238 0.071 - 0.107: 86 0.107 - 0.142: 21 0.142 - 0.178: 3 Chirality restraints: 1210 Sorted by residual: chirality pdb=" C1' DG D 0 " pdb=" O4' DG D 0 " pdb=" C2' DG D 0 " pdb=" N9 DG D 0 " both_signs ideal model delta sigma weight residual False 2.43 2.25 0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA ASP A 560 " pdb=" N ASP A 560 " pdb=" C ASP A 560 " pdb=" CB ASP A 560 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" C1' DG D -9 " pdb=" O4' DG D -9 " pdb=" C2' DG D -9 " pdb=" N9 DG D -9 " both_signs ideal model delta sigma weight residual False 2.43 2.28 0.15 2.00e-01 2.50e+01 5.45e-01 ... (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: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.620 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.030 ------------------------------------------------------------------------------- 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= 0.362 Angle : 0.587 9.011 10473 Z= 0.453 Chirality : 0.040 0.178 1210 Planarity : 0.004 0.042 951 Dihedral : 19.887 118.750 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 0.00451 / 0.36 ( 7339) covalent geometry : angle 0.57399 / 0.45 (10470) hydrogen bonds : bond 0.12160 / 7.07 ( 405) hydrogen bonds : angle 5.09844 / 2.89 ( 1085) metal coordination : bond 0.03038 / 1.77 ( 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 : 2.663 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: 0.8481 time to fit residues: 72.1742 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 : 0.206 ------------------------------------------------------------------------------- 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: 10.0000 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 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 = 0.3804 r_free = 0.3804 target = 0.136448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104237 restraints weight = 9791.127| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.48 r_work: 0.3196 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7343 Z= 0.195 Angle : 0.589 9.150 10473 Z= 0.333 Chirality : 0.040 0.184 1210 Planarity : 0.006 0.097 951 Dihedral : 20.615 116.089 1923 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.54 % Allowed : 16.88 % Favored : 79.58 % 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: 2.66 (0.34), residues: 590 helix: 2.96 (0.28), residues: 323 sheet: 1.89 (0.62), residues: 60 loop : -0.30 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 580 TYR 0.009 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 0.00388 / 0.20 ( 7339) covalent geometry : angle 0.58850 / 0.33 (10470) hydrogen bonds : bond 0.05314 / 3.11 ( 405) hydrogen bonds : angle 3.70276 / 2.09 ( 1085) metal coordination : bond 0.00335 / 0.19 ( 4) metal coordination : angle 1.37579 / 0.46 ( 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 : 0.178 Fit side-chains REVERT: A 63 MET cc_start: 0.8310 (ttt) cc_final: 0.8033 (ttp) REVERT: A 89 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8189 (pp) REVERT: A 160 ASP cc_start: 0.8179 (m-30) cc_final: 0.7976 (m-30) REVERT: A 172 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7394 (mm-40) REVERT: A 199 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7803 (tt0) REVERT: A 264 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9054 (mt) REVERT: A 325 GLU cc_start: 0.8317 (mp0) cc_final: 0.8101 (mp0) REVERT: A 416 LYS cc_start: 0.6793 (mttt) cc_final: 0.5480 (tttm) REVERT: A 458 ARG cc_start: 0.8771 (mmm160) cc_final: 0.8270 (mmm-85) REVERT: A 459 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8049 (mttp) REVERT: A 575 MET cc_start: 0.8614 (mtp) cc_final: 0.8222 (mtt) outliers start: 17 outliers final: 7 residues processed: 63 average time/residue: 0.8580 time to fit residues: 56.1924 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 : 0.187 ------------------------------------------------------------------------------- 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: 6.9990 chunk 59 optimal weight: 7.9990 chunk 7 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.135544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.103149 restraints weight = 9812.547| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.51 r_work: 0.3180 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7343 Z= 0.216 Angle : 0.589 9.246 10473 Z= 0.330 Chirality : 0.041 0.189 1210 Planarity : 0.005 0.082 951 Dihedral : 20.741 115.946 1921 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: 2.68 (0.34), residues: 590 helix: 2.99 (0.27), residues: 324 sheet: 1.71 (0.61), residues: 60 loop : -0.25 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 85 TYR 0.009 0.001 TYR A 42 PHE 0.007 0.001 PHE A 443 TRP 0.012 0.001 TRP A 232 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.22 ( 7339) covalent geometry : angle 0.58876 / 0.33 (10470) hydrogen bonds : bond 0.05242 / 3.09 ( 405) hydrogen bonds : angle 3.63844 / 2.05 ( 1085) metal coordination : bond 0.00318 / 0.20 ( 4) metal coordination : angle 1.00398 / 0.33 ( 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 66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.207 Fit side-chains REVERT: A 63 MET cc_start: 0.8339 (ttt) cc_final: 0.8057 (ttp) REVERT: A 89 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8004 (pp) REVERT: A 103 ARG cc_start: 0.8325 (mtp180) cc_final: 0.8040 (mtm180) REVERT: A 172 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7502 (mm-40) REVERT: A 199 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7911 (tp40) REVERT: A 416 LYS cc_start: 0.6764 (mttt) cc_final: 0.5420 (tttm) REVERT: A 458 ARG cc_start: 0.8728 (mmm160) cc_final: 0.8373 (mmm-85) REVERT: A 459 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8075 (mttp) REVERT: A 498 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: A 575 MET cc_start: 0.8625 (mtp) cc_final: 0.8243 (mtt) outliers start: 20 outliers final: 10 residues processed: 61 average time/residue: 0.8483 time to fit residues: 53.7959 Evaluate side-chains 57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 82 ILE 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 340 ILE 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 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: 0.2980 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.137312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.104809 restraints weight = 9792.682| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.51 r_work: 0.3226 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1496 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 : 0.539 8.334 10473 Z= 0.307 Chirality : 0.038 0.184 1210 Planarity : 0.004 0.058 951 Dihedral : 20.687 114.583 1919 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 2.88 (0.34), residues: 590 helix: 3.20 (0.27), residues: 324 sheet: 1.54 (0.60), residues: 62 loop : -0.18 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.008 0.001 TYR A 42 PHE 0.005 0.001 PHE A 155 TRP 0.010 0.001 TRP A 232 HIS 0.001 0.000 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 ( 7339) covalent geometry : angle 0.53939 / 0.31 (10470) hydrogen bonds : bond 0.04571 / 2.70 ( 405) hydrogen bonds : angle 3.40802 / 1.92 ( 1085) metal coordination : bond 0.00130 / 0.08 ( 4) metal coordination : angle 0.62865 / 0.21 ( 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 62 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.218 Fit side-chains REVERT: A 63 MET cc_start: 0.8328 (ttt) cc_final: 0.7978 (ttp) REVERT: A 89 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8236 (pp) REVERT: A 98 ARG cc_start: 0.8168 (mtp-110) cc_final: 0.7790 (mtm-85) REVERT: A 103 ARG cc_start: 0.8320 (mtp180) cc_final: 0.8116 (mtm180) REVERT: A 146 ARG cc_start: 0.8629 (mtp85) cc_final: 0.8111 (mtm-85) REVERT: A 172 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7374 (mm-40) REVERT: A 199 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7838 (tp40) REVERT: A 416 LYS cc_start: 0.6665 (mttt) cc_final: 0.5367 (tttm) REVERT: A 458 ARG cc_start: 0.8728 (mmm160) cc_final: 0.8339 (mmm-85) REVERT: A 498 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: A 575 MET cc_start: 0.8605 (mtp) cc_final: 0.8200 (mtt) REVERT: A 580 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8070 (mtm110) outliers start: 16 outliers final: 6 residues processed: 57 average time/residue: 0.8165 time to fit residues: 48.4196 Evaluate side-chains 54 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 7.9990 chunk 35 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 50.0000 chunk 64 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.137005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104710 restraints weight = 9770.722| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.49 r_work: 0.3206 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7343 Z= 0.177 Angle : 0.541 7.250 10473 Z= 0.308 Chirality : 0.039 0.184 1210 Planarity : 0.004 0.055 951 Dihedral : 20.705 113.895 1918 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.54 % Allowed : 19.38 % 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: 2.81 (0.34), residues: 590 helix: 3.16 (0.27), residues: 324 sheet: 1.46 (0.60), residues: 62 loop : -0.23 (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 0.007 0.001 PHE A 443 TRP 0.010 0.001 TRP A 232 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 ( 7339) covalent geometry : angle 0.54054 / 0.31 (10470) hydrogen bonds : bond 0.04788 / 2.83 ( 405) hydrogen bonds : angle 3.43050 / 1.93 ( 1085) metal coordination : bond 0.00228 / 0.13 ( 4) metal coordination : angle 0.70324 / 0.23 ( 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 62 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.126 Fit side-chains REVERT: A 63 MET cc_start: 0.8323 (ttt) cc_final: 0.8025 (ttp) REVERT: A 89 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8138 (pp) REVERT: A 98 ARG cc_start: 0.8155 (mtp-110) cc_final: 0.7637 (mtm110) REVERT: A 172 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7451 (mm-40) REVERT: A 199 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7859 (tp40) REVERT: A 335 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8808 (t0) REVERT: A 416 LYS cc_start: 0.6615 (mttt) cc_final: 0.5337 (tttm) REVERT: A 458 ARG cc_start: 0.8751 (mmm160) cc_final: 0.8346 (mmm-85) REVERT: A 498 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6333 (pm20) REVERT: A 575 MET cc_start: 0.8622 (mtp) cc_final: 0.8232 (mtt) REVERT: A 580 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7977 (mtm110) outliers start: 17 outliers final: 9 residues processed: 57 average time/residue: 0.8040 time to fit residues: 47.6520 Evaluate side-chains 57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 194 VAL Chi-restraints excluded: chain A residue 264 LEU 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 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: 0.9990 chunk 32 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 40.0000 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.136371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.103929 restraints weight = 9735.973| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.48 r_work: 0.3218 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7343 Z= 0.159 Angle : 0.540 6.974 10473 Z= 0.307 Chirality : 0.038 0.183 1210 Planarity : 0.004 0.046 951 Dihedral : 20.704 113.279 1918 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.33 % Allowed : 19.79 % 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: 2.88 (0.34), residues: 590 helix: 3.24 (0.27), residues: 324 sheet: 1.47 (0.59), residues: 62 loop : -0.22 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.001 0.000 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 ( 7339) covalent geometry : angle 0.53968 / 0.31 (10470) hydrogen bonds : bond 0.04587 / 2.71 ( 405) hydrogen bonds : angle 3.36493 / 1.89 ( 1085) metal coordination : bond 0.00202 / 0.12 ( 4) metal coordination : angle 0.66095 / 0.22 ( 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 65 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.214 Fit side-chains REVERT: A 63 MET cc_start: 0.8329 (ttt) cc_final: 0.8017 (ttp) REVERT: A 88 LYS cc_start: 0.8695 (tmmt) cc_final: 0.8406 (tppt) REVERT: A 172 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7424 (mm-40) REVERT: A 199 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7847 (tp40) REVERT: A 335 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8766 (t0) REVERT: A 367 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7830 (ttp-110) REVERT: A 413 LYS cc_start: 0.8121 (tttt) cc_final: 0.7086 (tptp) REVERT: A 416 LYS cc_start: 0.6584 (mttt) cc_final: 0.5321 (tttm) REVERT: A 458 ARG cc_start: 0.8768 (mmm160) cc_final: 0.8377 (mmm-85) REVERT: A 498 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: A 575 MET cc_start: 0.8575 (mtp) cc_final: 0.8181 (mtt) outliers start: 16 outliers final: 7 residues processed: 60 average time/residue: 0.7882 time to fit residues: 49.1768 Evaluate side-chains 56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 93 LEU Chi-restraints excluded: chain A residue 194 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 30.0000 chunk 40 optimal weight: 0.0070 chunk 55 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.1604 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.135991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.103571 restraints weight = 9771.873| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.49 r_work: 0.3199 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7343 Z= 0.194 Angle : 0.567 8.518 10473 Z= 0.318 Chirality : 0.040 0.185 1210 Planarity : 0.004 0.042 951 Dihedral : 20.727 113.118 1918 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.75 % Allowed : 19.79 % Favored : 76.46 % 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: 2.77 (0.34), residues: 590 helix: 3.16 (0.27), residues: 324 sheet: 1.40 (0.59), residues: 62 loop : -0.29 (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 0.007 0.001 PHE A 443 TRP 0.010 0.001 TRP A 232 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 ( 7339) covalent geometry : angle 0.56725 / 0.32 (10470) hydrogen bonds : bond 0.04853 / 2.87 ( 405) hydrogen bonds : angle 3.43399 / 1.92 ( 1085) metal coordination : bond 0.00265 / 0.16 ( 4) metal coordination : angle 0.73608 / 0.25 ( 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 66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.186 Fit side-chains REVERT: A 63 MET cc_start: 0.8301 (ttt) cc_final: 0.8015 (ttp) REVERT: A 98 ARG cc_start: 0.8131 (mtp-110) cc_final: 0.7636 (mtm110) REVERT: A 172 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7487 (mm-40) REVERT: A 199 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7864 (tp40) REVERT: A 335 ASP cc_start: 0.9036 (OUTLIER) cc_final: 0.8811 (t0) REVERT: A 367 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7849 (ttp-110) REVERT: A 413 LYS cc_start: 0.8125 (tttt) cc_final: 0.7089 (tptp) REVERT: A 416 LYS cc_start: 0.6670 (mttt) cc_final: 0.5358 (tttm) REVERT: A 458 ARG cc_start: 0.8770 (mmm160) cc_final: 0.8373 (mmm-85) REVERT: A 498 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6326 (mp0) REVERT: A 575 MET cc_start: 0.8592 (mtp) cc_final: 0.8205 (mtt) outliers start: 18 outliers final: 11 residues processed: 60 average time/residue: 0.7840 time to fit residues: 48.9111 Evaluate side-chains 61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 93 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 360 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.135877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103588 restraints weight = 9882.387| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.50 r_work: 0.3202 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7343 Z= 0.188 Angle : 0.565 6.887 10473 Z= 0.319 Chirality : 0.039 0.182 1210 Planarity : 0.004 0.039 951 Dihedral : 20.751 113.036 1918 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.96 % Allowed : 20.00 % 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: 2.75 (0.34), residues: 590 helix: 3.16 (0.27), residues: 324 sheet: 1.38 (0.60), residues: 62 loop : -0.32 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 499 TYR 0.009 0.001 TYR A 42 PHE 0.006 0.001 PHE A 443 TRP 0.011 0.001 TRP A 232 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 ( 7339) covalent geometry : angle 0.56522 / 0.32 (10470) hydrogen bonds : bond 0.04815 / 2.85 ( 405) hydrogen bonds : angle 3.41341 / 1.91 ( 1085) metal coordination : bond 0.00241 / 0.15 ( 4) metal coordination : angle 0.76496 / 0.25 ( 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 67 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.217 Fit side-chains REVERT: A 63 MET cc_start: 0.8284 (ttt) cc_final: 0.7989 (ttp) REVERT: A 88 LYS cc_start: 0.8636 (tmmt) cc_final: 0.8335 (tppt) REVERT: A 98 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7634 (mtm110) REVERT: A 172 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7470 (mm-40) REVERT: A 335 ASP cc_start: 0.9038 (OUTLIER) cc_final: 0.8805 (t0) REVERT: A 367 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7851 (ttp-110) REVERT: A 413 LYS cc_start: 0.8136 (tttt) cc_final: 0.7125 (tptp) REVERT: A 416 LYS cc_start: 0.6676 (mttt) cc_final: 0.5324 (tttm) REVERT: A 458 ARG cc_start: 0.8760 (mmm160) cc_final: 0.8333 (mmm-85) REVERT: A 498 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6294 (mp0) REVERT: A 575 MET cc_start: 0.8588 (mtp) cc_final: 0.8205 (mtt) outliers start: 19 outliers final: 10 residues processed: 62 average time/residue: 0.8083 time to fit residues: 52.2083 Evaluate side-chains 59 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 93 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 194 VAL 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 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: 4.9990 chunk 45 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 40 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.137551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105079 restraints weight = 9820.757| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.50 r_work: 0.3229 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7343 Z= 0.140 Angle : 0.536 8.630 10473 Z= 0.304 Chirality : 0.037 0.181 1210 Planarity : 0.004 0.037 951 Dihedral : 20.722 111.942 1918 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.33 % Allowed : 20.83 % Favored : 75.83 % 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: 2.98 (0.34), residues: 590 helix: 3.35 (0.27), residues: 324 sheet: 1.42 (0.59), residues: 62 loop : -0.20 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 103 TYR 0.008 0.001 TYR A 42 PHE 0.005 0.001 PHE A 155 TRP 0.011 0.001 TRP A 232 HIS 0.001 0.000 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 ( 7339) covalent geometry : angle 0.53621 / 0.30 (10470) hydrogen bonds : bond 0.04428 / 2.62 ( 405) hydrogen bonds : angle 3.28242 / 1.84 ( 1085) metal coordination : bond 0.00146 / 0.08 ( 4) metal coordination : angle 0.60545 / 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 64 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.291 Fit side-chains REVERT: A 63 MET cc_start: 0.8280 (ttt) cc_final: 0.7996 (ttp) REVERT: A 88 LYS cc_start: 0.8668 (tmmt) cc_final: 0.8361 (tppt) REVERT: A 98 ARG cc_start: 0.8138 (mtp-110) cc_final: 0.7616 (mtm110) REVERT: A 172 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7391 (mm-40) REVERT: A 367 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7806 (ttp-110) REVERT: A 413 LYS cc_start: 0.8101 (tttt) cc_final: 0.7103 (tptp) REVERT: A 416 LYS cc_start: 0.6594 (mttt) cc_final: 0.5289 (tttm) REVERT: A 458 ARG cc_start: 0.8768 (mmm160) cc_final: 0.8372 (mmm-85) REVERT: A 498 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6356 (mp0) REVERT: A 575 MET cc_start: 0.8595 (mtp) cc_final: 0.8207 (mtt) REVERT: A 580 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7982 (mtm110) outliers start: 16 outliers final: 10 residues processed: 60 average time/residue: 0.8036 time to fit residues: 49.9861 Evaluate side-chains 58 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 93 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 191 THR 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 530 MET Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 580 ARG 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: 8.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 9 optimal weight: 40.0000 chunk 65 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.138268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.105952 restraints weight = 9679.725| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.48 r_work: 0.3247 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7343 Z= 0.140 Angle : 0.544 11.124 10473 Z= 0.307 Chirality : 0.037 0.179 1210 Planarity : 0.005 0.084 951 Dihedral : 20.674 110.713 1918 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.08 % Allowed : 22.50 % Favored : 75.42 % 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: 2.98 (0.34), residues: 590 helix: 3.34 (0.27), residues: 324 sheet: 1.47 (0.59), residues: 62 loop : -0.21 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 85 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 0.001 0.000 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 ( 7339) covalent geometry : angle 0.54415 / 0.31 (10470) hydrogen bonds : bond 0.04318 / 2.56 ( 405) hydrogen bonds : angle 3.23310 / 1.81 ( 1085) metal coordination : bond 0.00155 / 0.09 ( 4) metal coordination : angle 0.50818 / 0.17 ( 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 : 0.216 Fit side-chains REVERT: A 63 MET cc_start: 0.8258 (ttt) cc_final: 0.7952 (ttp) REVERT: A 88 LYS cc_start: 0.8632 (tmmt) cc_final: 0.8370 (tppt) REVERT: A 98 ARG cc_start: 0.8130 (mtp-110) cc_final: 0.7610 (mtm110) REVERT: A 172 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7369 (mm-40) REVERT: A 367 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7775 (ttp-110) REVERT: A 413 LYS cc_start: 0.8054 (tttt) cc_final: 0.7067 (tptp) REVERT: A 416 LYS cc_start: 0.6598 (mttt) cc_final: 0.5291 (tttm) REVERT: A 458 ARG cc_start: 0.8769 (mmm160) cc_final: 0.8331 (mmm-85) REVERT: A 497 MET cc_start: 0.7965 (mmm) cc_final: 0.7746 (tpt) REVERT: A 498 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: A 575 MET cc_start: 0.8577 (mtp) cc_final: 0.8199 (mtt) REVERT: A 580 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7961 (mtm110) outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.9319 time to fit residues: 51.1599 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 : 0.210 ------------------------------------------------------------------------------- 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 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 530 MET Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 580 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 47 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 9 optimal weight: 40.0000 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.136480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.103998 restraints weight = 9746.027| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.50 r_work: 0.3213 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7343 Z= 0.176 Angle : 0.566 10.836 10473 Z= 0.315 Chirality : 0.039 0.176 1210 Planarity : 0.005 0.079 951 Dihedral : 20.705 111.129 1918 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.71 % Allowed : 21.46 % Favored : 75.83 % 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: 3.24 (0.27), residues: 324 sheet: 1.38 (0.58), residues: 62 loop : -0.26 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 85 TYR 0.008 0.001 TYR A 42 PHE 0.007 0.001 PHE A 443 TRP 0.010 0.001 TRP A 232 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 ( 7339) covalent geometry : angle 0.56614 / 0.31 (10470) hydrogen bonds : bond 0.04635 / 2.74 ( 405) hydrogen bonds : angle 3.32994 / 1.86 ( 1085) metal coordination : bond 0.00244 / 0.15 ( 4) metal coordination : angle 0.67459 / 0.22 ( 3) =============================================================================== Job complete usr+sys time: 2423.99 seconds wall clock time: 42 minutes 3.46 seconds (2523.46 seconds total)