Starting phenix.real_space_refine on Wed Sep 17 23:16:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vvd_43555/09_2025/8vvd_43555_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vvd_43555/09_2025/8vvd_43555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vvd_43555/09_2025/8vvd_43555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vvd_43555/09_2025/8vvd_43555.map" model { file = "/net/cci-nas-00/data/ceres_data/8vvd_43555/09_2025/8vvd_43555_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vvd_43555/09_2025/8vvd_43555_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6069 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 23 5.49 5 S 35 5.16 5 C 4354 2.51 5 N 1211 2.21 5 O 1357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6980 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6513 Classifications: {'peptide': 850} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 35, 'TRANS': 814} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 404 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 23, 'TRP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 9, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 236 Chain: "B" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 467 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna2p': 8, 'rna3p': 14} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {' U:plan': 1, ' U%rna3p_pyr:plan': 2} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 1.97, per 1000 atoms: 0.28 Number of scatterers: 6980 At special positions: 0 Unit cell: (74.7, 106.24, 112.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 23 15.00 O 1357 8.00 N 1211 7.00 C 4354 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: 0.65 Conformation dependent library (CDL) restraints added in 444.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1618 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 4 sheets defined 56.0% alpha, 12.6% beta 3 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 62 through 82 removed outlier: 3.843A pdb=" N GLY A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.869A pdb=" N THR A 107 " --> pdb=" O HIS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 196 through 208 removed outlier: 4.220A pdb=" N LYS A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 214 through 224 Processing helix chain 'A' and resid 237 through 253 removed outlier: 4.863A pdb=" N THR A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLN A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 removed outlier: 3.560A pdb=" N ALA A 258 " --> pdb=" O LYS A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 267 through 282 Processing helix chain 'A' and resid 314 through 324 removed outlier: 3.632A pdb=" N LEU A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 356 Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.753A pdb=" N SER A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 432 through 450 removed outlier: 3.782A pdb=" N GLU A 436 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Proline residue: A 446 - end of helix removed outlier: 3.579A pdb=" N ARG A 450 " --> pdb=" O PRO A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.346A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 456' Processing helix chain 'A' and resid 457 through 467 removed outlier: 3.622A pdb=" N VAL A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 499 through 513 removed outlier: 3.881A pdb=" N GLN A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.766A pdb=" N SER A 518 " --> pdb=" O MET A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 removed outlier: 3.961A pdb=" N GLN A 535 " --> pdb=" O PRO A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 removed outlier: 3.663A pdb=" N THR A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 605 removed outlier: 3.885A pdb=" N ALA A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 638 through 648 Processing helix chain 'A' and resid 652 through 660 Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.601A pdb=" N HIS A 694 " --> pdb=" O PRO A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 714 Processing helix chain 'A' and resid 716 through 729 Processing helix chain 'A' and resid 740 through 751 Processing helix chain 'A' and resid 758 through 775 removed outlier: 3.916A pdb=" N GLN A 773 " --> pdb=" O GLU A 769 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG A 774 " --> pdb=" O LYS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 786 Processing helix chain 'A' and resid 789 through 811 Processing helix chain 'A' and resid 820 through 824 Processing helix chain 'A' and resid 829 through 841 Processing helix chain 'A' and resid 908 through 916 removed outlier: 3.600A pdb=" N LEU A 912 " --> pdb=" O SER A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 965 Processing helix chain 'A' and resid 976 through 989 removed outlier: 3.628A pdb=" N LEU A 982 " --> pdb=" O ASP A 978 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 299 through 301 removed outlier: 7.052A pdb=" N GLY A 293 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N THR A 313 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLN A 295 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ARG A 260 " --> pdb=" O HIS A 332 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL A 334 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 262 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ILE A 386 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL A 229 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE A 388 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER A 231 " --> pdb=" O ILE A 388 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 395 through 398 removed outlier: 6.259A pdb=" N VAL A 396 " --> pdb=" O CYS A 613 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N HIS A 615 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR A 398 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA A 492 " --> pdb=" O TYR A 567 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE A 569 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A 494 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 580 removed outlier: 6.784A pdb=" N SER A 586 " --> pdb=" O ARG A 895 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE A 899 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A 861 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE A 871 " --> pdb=" O VAL A 859 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N VAL A 859 " --> pdb=" O ILE A 871 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 919 through 924 360 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 6 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2203 1.34 - 1.46: 1468 1.46 - 1.58: 3383 1.58 - 1.70: 43 1.70 - 1.82: 55 Bond restraints: 7152 Sorted by residual: bond pdb=" CA TYR A 441 " pdb=" C TYR A 441 " ideal model delta sigma weight residual 1.524 1.469 0.054 1.32e-02 5.74e+03 1.70e+01 bond pdb=" P U B 18 " pdb=" O5' U B 18 " ideal model delta sigma weight residual 1.593 1.632 -0.039 1.50e-02 4.44e+03 6.65e+00 bond pdb=" O5' U B 18 " pdb=" C5' U B 18 " ideal model delta sigma weight residual 1.420 1.456 -0.036 1.50e-02 4.44e+03 5.82e+00 bond pdb=" N GLU A 433 " pdb=" CA GLU A 433 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.73e+00 bond pdb=" N ASP A 924 " pdb=" CA ASP A 924 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.23e-02 6.61e+03 5.67e+00 ... (remaining 7147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 9651 2.33 - 4.66: 129 4.66 - 7.00: 22 7.00 - 9.33: 5 9.33 - 11.66: 2 Bond angle restraints: 9809 Sorted by residual: angle pdb=" N PRO A 178 " pdb=" CA PRO A 178 " pdb=" CB PRO A 178 " ideal model delta sigma weight residual 103.25 110.05 -6.80 1.05e+00 9.07e-01 4.19e+01 angle pdb=" N GLU A 443 " pdb=" CA GLU A 443 " pdb=" C GLU A 443 " ideal model delta sigma weight residual 114.12 105.16 8.96 1.39e+00 5.18e-01 4.16e+01 angle pdb=" C GLN A 432 " pdb=" CA GLN A 432 " pdb=" CB GLN A 432 " ideal model delta sigma weight residual 116.63 110.35 6.28 1.16e+00 7.43e-01 2.93e+01 angle pdb=" C ASP A 926 " pdb=" CA ASP A 926 " pdb=" CB ASP A 926 " ideal model delta sigma weight residual 109.56 101.88 7.68 1.65e+00 3.67e-01 2.16e+01 angle pdb=" N ARG A 444 " pdb=" CA ARG A 444 " pdb=" C ARG A 444 " ideal model delta sigma weight residual 114.12 108.12 6.00 1.39e+00 5.18e-01 1.86e+01 ... (remaining 9804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 3658 17.72 - 35.44: 462 35.44 - 53.15: 183 53.15 - 70.87: 76 70.87 - 88.59: 17 Dihedral angle restraints: 4396 sinusoidal: 1905 harmonic: 2491 Sorted by residual: dihedral pdb=" C4' U B 18 " pdb=" C3' U B 18 " pdb=" C2' U B 18 " pdb=" C1' U B 18 " ideal model delta sinusoidal sigma weight residual 36.00 -38.01 74.01 1 8.00e+00 1.56e-02 1.09e+02 dihedral pdb=" C4' U B 19 " pdb=" C3' U B 19 " pdb=" C2' U B 19 " pdb=" C1' U B 19 " ideal model delta sinusoidal sigma weight residual 36.00 -35.89 71.89 1 8.00e+00 1.56e-02 1.03e+02 dihedral pdb=" C5' U B 18 " pdb=" C4' U B 18 " pdb=" C3' U B 18 " pdb=" O3' U B 18 " ideal model delta sinusoidal sigma weight residual 82.00 152.06 -70.06 1 8.00e+00 1.56e-02 9.89e+01 ... (remaining 4393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1133 0.113 - 0.226: 30 0.226 - 0.340: 2 0.340 - 0.453: 1 0.453 - 0.566: 2 Chirality restraints: 1168 Sorted by residual: chirality pdb=" P U B 18 " pdb=" OP1 U B 18 " pdb=" OP2 U B 18 " pdb=" O5' U B 18 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" P G B 20 " pdb=" OP1 G B 20 " pdb=" OP2 G B 20 " pdb=" O5' G B 20 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" P U B 19 " pdb=" OP1 U B 19 " pdb=" OP2 U B 19 " pdb=" O5' U B 19 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 1165 not shown) Planarity restraints: 1168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 444 " -1.030 9.50e-02 1.11e+02 4.62e-01 1.29e+02 pdb=" NE ARG A 444 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG A 444 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 444 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 444 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 749 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" CD GLU A 749 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU A 749 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 749 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 500 " -0.009 2.00e-02 2.50e+03 1.37e-02 4.67e+00 pdb=" CG TRP A 500 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 500 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 500 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 500 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 500 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 500 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 500 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 500 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 500 " -0.000 2.00e-02 2.50e+03 ... (remaining 1165 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1633 2.79 - 3.32: 6646 3.32 - 3.84: 11754 3.84 - 4.37: 13504 4.37 - 4.90: 23013 Nonbonded interactions: 56550 Sorted by model distance: nonbonded pdb=" O VAL A 88 " pdb=" OG SER A 940 " model vdw 2.260 3.040 nonbonded pdb=" OE2 GLU A 401 " pdb=" OH TYR A 448 " model vdw 2.287 3.040 nonbonded pdb=" N GLN A 922 " pdb=" OE1 GLN A 922 " model vdw 2.305 3.120 nonbonded pdb=" OE1 GLU A 805 " pdb=" NE ARG A 816 " model vdw 2.309 3.120 nonbonded pdb=" NE2 HIS A 758 " pdb=" OD2 ASP A 903 " model vdw 2.309 3.120 ... (remaining 56545 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.780 Find NCS groups from input model: 0.040 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:9.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 0.004 0.096 7152 Z= 0.204 Angle : 0.682 11.659 9809 Z= 0.390 Chirality : 0.053 0.566 1168 Planarity : 0.014 0.462 1168 Dihedral : 20.264 88.589 2778 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.44 % Favored : 96.32 % Rotamer: Outliers : 4.84 % Allowed : 30.06 % Favored : 65.10 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.31), residues: 842 helix: 1.64 (0.26), residues: 430 sheet: 1.09 (0.52), residues: 114 loop : -0.42 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 747 TYR 0.013 0.001 TYR A 441 PHE 0.009 0.001 PHE A 914 TRP 0.035 0.002 TRP A 500 HIS 0.005 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7152) covalent geometry : angle 0.68245 ( 9809) hydrogen bonds : bond 0.15994 ( 366) hydrogen bonds : angle 5.96432 ( 1044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.213 Fit side-chains REVERT: A 340 GLU cc_start: 0.8396 (pp20) cc_final: 0.7882 (pp20) REVERT: A 467 MET cc_start: 0.8459 (mmt) cc_final: 0.8239 (tpt) REVERT: A 784 TRP cc_start: 0.8406 (t60) cc_final: 0.8153 (t60) outliers start: 33 outliers final: 17 residues processed: 92 average time/residue: 0.5406 time to fit residues: 52.6484 Evaluate side-chains 61 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 884 ASN Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 985 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 806 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.085013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.062099 restraints weight = 16945.557| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.11 r_work: 0.2841 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7152 Z= 0.131 Angle : 0.561 7.344 9809 Z= 0.292 Chirality : 0.042 0.174 1168 Planarity : 0.004 0.042 1168 Dihedral : 15.077 80.676 1302 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.68 % Favored : 96.08 % Rotamer: Outliers : 5.43 % Allowed : 28.59 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.30), residues: 842 helix: 1.74 (0.26), residues: 438 sheet: 0.77 (0.49), residues: 124 loop : -0.46 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 444 TYR 0.008 0.001 TYR A 902 PHE 0.009 0.001 PHE A 516 TRP 0.015 0.002 TRP A 768 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7152) covalent geometry : angle 0.56055 ( 9809) hydrogen bonds : bond 0.03953 ( 366) hydrogen bonds : angle 4.35268 ( 1044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 50 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8411 (pp20) cc_final: 0.7730 (pp20) REVERT: A 467 MET cc_start: 0.8890 (mmt) cc_final: 0.8678 (tpt) REVERT: A 582 GLN cc_start: 0.9337 (OUTLIER) cc_final: 0.9122 (tp40) REVERT: A 604 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8529 (tpp80) REVERT: A 757 ASP cc_start: 0.8824 (t0) cc_final: 0.8502 (m-30) REVERT: A 784 TRP cc_start: 0.8718 (t60) cc_final: 0.8266 (t60) outliers start: 37 outliers final: 17 residues processed: 83 average time/residue: 0.5377 time to fit residues: 47.3163 Evaluate side-chains 62 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 946 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.084896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.061782 restraints weight = 17029.194| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.14 r_work: 0.2832 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7152 Z= 0.123 Angle : 0.531 7.866 9809 Z= 0.272 Chirality : 0.041 0.166 1168 Planarity : 0.004 0.045 1168 Dihedral : 14.630 74.965 1288 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.44 % Rotamer: Outliers : 5.43 % Allowed : 27.42 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.31), residues: 842 helix: 1.99 (0.26), residues: 438 sheet: 0.58 (0.49), residues: 124 loop : -0.39 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 747 TYR 0.009 0.001 TYR A 456 PHE 0.006 0.001 PHE A 376 TRP 0.013 0.001 TRP A 768 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7152) covalent geometry : angle 0.53072 ( 9809) hydrogen bonds : bond 0.03425 ( 366) hydrogen bonds : angle 4.05023 ( 1044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 46 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 203 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8817 (mp10) REVERT: A 437 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8479 (ttpp) REVERT: A 467 MET cc_start: 0.8935 (mmt) cc_final: 0.8720 (tpt) REVERT: A 486 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8476 (mt) REVERT: A 582 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.9122 (tp40) REVERT: A 757 ASP cc_start: 0.8959 (t0) cc_final: 0.8591 (m-30) REVERT: A 784 TRP cc_start: 0.8691 (t60) cc_final: 0.8240 (t60) REVERT: A 960 GLN cc_start: 0.8224 (tt0) cc_final: 0.7923 (tp-100) REVERT: A 977 ARG cc_start: 0.7784 (mpt-90) cc_final: 0.7583 (mmt-90) outliers start: 37 outliers final: 15 residues processed: 81 average time/residue: 0.5745 time to fit residues: 49.1949 Evaluate side-chains 62 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 946 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.084828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.061828 restraints weight = 17022.417| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.11 r_work: 0.2830 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7152 Z= 0.117 Angle : 0.515 8.757 9809 Z= 0.265 Chirality : 0.041 0.156 1168 Planarity : 0.004 0.047 1168 Dihedral : 14.481 74.123 1287 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 4.69 % Allowed : 28.30 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.31), residues: 842 helix: 2.02 (0.25), residues: 442 sheet: 0.31 (0.47), residues: 131 loop : -0.26 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 943 TYR 0.023 0.001 TYR A 199 PHE 0.008 0.001 PHE A 205 TRP 0.013 0.001 TRP A 500 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7152) covalent geometry : angle 0.51508 ( 9809) hydrogen bonds : bond 0.03206 ( 366) hydrogen bonds : angle 3.93932 ( 1044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 49 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 437 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8451 (ttpp) REVERT: A 467 MET cc_start: 0.8888 (mmt) cc_final: 0.8686 (tpt) REVERT: A 486 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8563 (mt) REVERT: A 582 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.9089 (tp40) REVERT: A 604 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8803 (tpp80) REVERT: A 757 ASP cc_start: 0.8959 (t0) cc_final: 0.8595 (m-30) REVERT: A 784 TRP cc_start: 0.8687 (t60) cc_final: 0.8230 (t60) REVERT: A 841 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8539 (pp) REVERT: A 960 GLN cc_start: 0.8206 (tt0) cc_final: 0.7935 (tp-100) outliers start: 32 outliers final: 15 residues processed: 79 average time/residue: 0.5298 time to fit residues: 44.3876 Evaluate side-chains 62 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 946 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 69 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 24 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 925 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.083818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.060726 restraints weight = 17226.059| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.13 r_work: 0.2805 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7152 Z= 0.144 Angle : 0.522 9.402 9809 Z= 0.268 Chirality : 0.041 0.143 1168 Planarity : 0.004 0.048 1168 Dihedral : 14.282 71.700 1285 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.80 % Favored : 96.08 % Rotamer: Outliers : 5.13 % Allowed : 28.15 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.31), residues: 842 helix: 2.08 (0.25), residues: 442 sheet: 0.39 (0.45), residues: 137 loop : -0.41 (0.41), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 747 TYR 0.011 0.001 TYR A 842 PHE 0.005 0.001 PHE A 376 TRP 0.012 0.001 TRP A 500 HIS 0.004 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7152) covalent geometry : angle 0.52190 ( 9809) hydrogen bonds : bond 0.03310 ( 366) hydrogen bonds : angle 3.92563 ( 1044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 46 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 437 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8448 (ttpp) REVERT: A 486 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8616 (mt) REVERT: A 582 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.9100 (tp40) REVERT: A 604 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8825 (tpp80) REVERT: A 757 ASP cc_start: 0.9018 (t0) cc_final: 0.8520 (m-30) REVERT: A 784 TRP cc_start: 0.8671 (t60) cc_final: 0.8217 (t60) REVERT: A 841 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8508 (pp) REVERT: A 908 SER cc_start: 0.7502 (OUTLIER) cc_final: 0.6997 (p) REVERT: A 960 GLN cc_start: 0.8216 (tt0) cc_final: 0.7926 (tp-100) outliers start: 35 outliers final: 20 residues processed: 77 average time/residue: 0.5324 time to fit residues: 43.3306 Evaluate side-chains 68 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 42 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 985 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.0570 chunk 48 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.084905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.061860 restraints weight = 17208.406| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.11 r_work: 0.2839 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7152 Z= 0.102 Angle : 0.505 10.139 9809 Z= 0.259 Chirality : 0.040 0.134 1168 Planarity : 0.003 0.048 1168 Dihedral : 14.241 69.071 1285 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.04 % Favored : 95.84 % Rotamer: Outliers : 4.11 % Allowed : 28.59 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.31), residues: 842 helix: 2.18 (0.25), residues: 444 sheet: 0.34 (0.47), residues: 126 loop : -0.28 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 747 TYR 0.011 0.001 TYR A 199 PHE 0.006 0.001 PHE A 516 TRP 0.016 0.001 TRP A 500 HIS 0.003 0.000 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7152) covalent geometry : angle 0.50503 ( 9809) hydrogen bonds : bond 0.02974 ( 366) hydrogen bonds : angle 3.78864 ( 1044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 45 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 437 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8445 (ttpp) REVERT: A 486 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8611 (mt) REVERT: A 604 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8736 (tpp80) REVERT: A 757 ASP cc_start: 0.8988 (t0) cc_final: 0.8532 (m-30) REVERT: A 784 TRP cc_start: 0.8634 (t60) cc_final: 0.8181 (t60) REVERT: A 841 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8586 (pp) REVERT: A 908 SER cc_start: 0.7521 (OUTLIER) cc_final: 0.7014 (p) REVERT: A 960 GLN cc_start: 0.8159 (tt0) cc_final: 0.7923 (tp-100) REVERT: A 977 ARG cc_start: 0.7797 (mpt-90) cc_final: 0.7383 (mmt-90) outliers start: 28 outliers final: 17 residues processed: 69 average time/residue: 0.4662 time to fit residues: 34.4170 Evaluate side-chains 64 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 946 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 925 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.084258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.061036 restraints weight = 17132.672| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.10 r_work: 0.2827 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7152 Z= 0.118 Angle : 0.525 10.668 9809 Z= 0.262 Chirality : 0.041 0.149 1168 Planarity : 0.003 0.048 1168 Dihedral : 14.177 65.895 1284 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.21 % Favored : 96.67 % Rotamer: Outliers : 5.13 % Allowed : 27.71 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.31), residues: 842 helix: 2.20 (0.25), residues: 444 sheet: 0.46 (0.46), residues: 132 loop : -0.42 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 747 TYR 0.009 0.001 TYR A 456 PHE 0.008 0.001 PHE A 765 TRP 0.017 0.001 TRP A 500 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7152) covalent geometry : angle 0.52535 ( 9809) hydrogen bonds : bond 0.03115 ( 366) hydrogen bonds : angle 3.78057 ( 1044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 44 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 604 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8755 (tpp80) REVERT: A 757 ASP cc_start: 0.8995 (t0) cc_final: 0.8487 (m-30) REVERT: A 784 TRP cc_start: 0.8624 (t60) cc_final: 0.8164 (t60) REVERT: A 908 SER cc_start: 0.7558 (OUTLIER) cc_final: 0.7052 (p) REVERT: A 933 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8887 (m-30) REVERT: A 960 GLN cc_start: 0.8170 (tt0) cc_final: 0.7927 (tp-100) outliers start: 35 outliers final: 19 residues processed: 74 average time/residue: 0.5172 time to fit residues: 40.7222 Evaluate side-chains 63 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 946 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 925 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.084491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.061388 restraints weight = 17407.637| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.15 r_work: 0.2827 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7152 Z= 0.112 Angle : 0.544 11.852 9809 Z= 0.267 Chirality : 0.041 0.158 1168 Planarity : 0.004 0.048 1168 Dihedral : 14.041 64.340 1278 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.33 % Favored : 96.56 % Rotamer: Outliers : 4.25 % Allowed : 28.74 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.31), residues: 842 helix: 2.24 (0.25), residues: 444 sheet: 0.33 (0.48), residues: 126 loop : -0.29 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 747 TYR 0.011 0.001 TYR A 842 PHE 0.003 0.001 PHE A 376 TRP 0.017 0.001 TRP A 500 HIS 0.003 0.000 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7152) covalent geometry : angle 0.54354 ( 9809) hydrogen bonds : bond 0.03031 ( 366) hydrogen bonds : angle 3.75788 ( 1044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 42 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 604 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8759 (tpp80) REVERT: A 757 ASP cc_start: 0.9014 (t0) cc_final: 0.8507 (m-30) REVERT: A 784 TRP cc_start: 0.8627 (t60) cc_final: 0.8169 (t60) REVERT: A 908 SER cc_start: 0.7548 (OUTLIER) cc_final: 0.7040 (p) REVERT: A 933 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8867 (m-30) REVERT: A 960 GLN cc_start: 0.8159 (tt0) cc_final: 0.7915 (tp-100) REVERT: A 977 ARG cc_start: 0.7729 (mpt180) cc_final: 0.7429 (mmt-90) REVERT: A 978 ASP cc_start: 0.8032 (t0) cc_final: 0.7824 (t0) outliers start: 29 outliers final: 18 residues processed: 67 average time/residue: 0.4976 time to fit residues: 35.5809 Evaluate side-chains 62 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 946 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 77 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 0.0980 chunk 25 optimal weight: 0.0010 chunk 71 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 0.0670 chunk 61 optimal weight: 0.3980 chunk 76 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 0.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.085560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.062686 restraints weight = 17294.475| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.12 r_work: 0.2856 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7152 Z= 0.090 Angle : 0.530 11.904 9809 Z= 0.262 Chirality : 0.040 0.155 1168 Planarity : 0.003 0.049 1168 Dihedral : 14.052 63.820 1278 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.21 % Favored : 96.67 % Rotamer: Outliers : 2.93 % Allowed : 30.35 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.31), residues: 842 helix: 2.31 (0.25), residues: 444 sheet: 0.40 (0.48), residues: 126 loop : -0.28 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 747 TYR 0.007 0.001 TYR A 842 PHE 0.004 0.001 PHE A 914 TRP 0.017 0.001 TRP A 500 HIS 0.002 0.000 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 7152) covalent geometry : angle 0.52994 ( 9809) hydrogen bonds : bond 0.02766 ( 366) hydrogen bonds : angle 3.69263 ( 1044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 604 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8769 (tpp80) REVERT: A 757 ASP cc_start: 0.9006 (t0) cc_final: 0.8515 (m-30) REVERT: A 784 TRP cc_start: 0.8615 (t60) cc_final: 0.8154 (t60) REVERT: A 908 SER cc_start: 0.7506 (OUTLIER) cc_final: 0.7011 (p) REVERT: A 933 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8855 (m-30) REVERT: A 960 GLN cc_start: 0.8113 (tt0) cc_final: 0.7881 (tp-100) REVERT: A 964 GLU cc_start: 0.8533 (tt0) cc_final: 0.8082 (tp30) REVERT: A 977 ARG cc_start: 0.7658 (mpt180) cc_final: 0.7347 (mmt-90) REVERT: A 978 ASP cc_start: 0.7971 (t0) cc_final: 0.7767 (t0) outliers start: 20 outliers final: 14 residues processed: 61 average time/residue: 0.5314 time to fit residues: 34.4541 Evaluate side-chains 59 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 946 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 0 optimal weight: 80.0000 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 33 optimal weight: 0.0030 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 925 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.085233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.062395 restraints weight = 17315.657| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.10 r_work: 0.2853 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7152 Z= 0.099 Angle : 0.538 12.614 9809 Z= 0.266 Chirality : 0.040 0.147 1168 Planarity : 0.003 0.048 1168 Dihedral : 14.029 63.814 1278 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.21 % Favored : 96.67 % Rotamer: Outliers : 2.79 % Allowed : 31.09 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.31), residues: 842 helix: 2.33 (0.25), residues: 444 sheet: 0.37 (0.48), residues: 126 loop : -0.26 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 747 TYR 0.011 0.001 TYR A 842 PHE 0.004 0.001 PHE A 205 TRP 0.021 0.001 TRP A 500 HIS 0.002 0.000 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 7152) covalent geometry : angle 0.53844 ( 9809) hydrogen bonds : bond 0.02794 ( 366) hydrogen bonds : angle 3.69439 ( 1044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 467 MET cc_start: 0.8844 (mmm) cc_final: 0.8426 (tpt) REVERT: A 604 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8789 (tpp80) REVERT: A 757 ASP cc_start: 0.9013 (t0) cc_final: 0.8506 (m-30) REVERT: A 784 TRP cc_start: 0.8595 (t60) cc_final: 0.8298 (t60) REVERT: A 908 SER cc_start: 0.7517 (OUTLIER) cc_final: 0.7026 (p) REVERT: A 933 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8880 (m-30) REVERT: A 960 GLN cc_start: 0.8100 (tt0) cc_final: 0.7882 (tp-100) REVERT: A 964 GLU cc_start: 0.8531 (tt0) cc_final: 0.8099 (tp30) REVERT: A 977 ARG cc_start: 0.7664 (mpt180) cc_final: 0.7314 (mmt-90) outliers start: 19 outliers final: 13 residues processed: 58 average time/residue: 0.5185 time to fit residues: 32.0858 Evaluate side-chains 58 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 933 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 80.0000 chunk 58 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 68 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 925 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.085358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.062236 restraints weight = 17394.746| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.15 r_work: 0.2851 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 7152 Z= 0.223 Angle : 0.973 59.200 9809 Z= 0.561 Chirality : 0.044 0.597 1168 Planarity : 0.003 0.048 1168 Dihedral : 14.008 63.812 1276 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.09 % Favored : 96.67 % Rotamer: Outliers : 3.08 % Allowed : 30.79 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.31), residues: 842 helix: 2.33 (0.25), residues: 444 sheet: 0.37 (0.48), residues: 126 loop : -0.26 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 94 TYR 0.011 0.001 TYR A 842 PHE 0.003 0.001 PHE A 205 TRP 0.018 0.001 TRP A 500 HIS 0.002 0.000 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7152) covalent geometry : angle 0.97317 ( 9809) hydrogen bonds : bond 0.02819 ( 366) hydrogen bonds : angle 3.69701 ( 1044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2037.88 seconds wall clock time: 35 minutes 39.64 seconds (2139.64 seconds total)