Starting phenix.real_space_refine on Tue Mar 11 15:09:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kx7_23061/03_2025/7kx7_23061.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kx7_23061/03_2025/7kx7_23061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kx7_23061/03_2025/7kx7_23061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kx7_23061/03_2025/7kx7_23061.map" model { file = "/net/cci-nas-00/data/ceres_data/7kx7_23061/03_2025/7kx7_23061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kx7_23061/03_2025/7kx7_23061.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.028 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 82 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 3676 2.51 5 N 1035 2.21 5 O 1075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5828 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5679 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 38, 'TRANS': 690} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 106 Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Classifications: {'RNA': 7} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p': 1, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" 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} Time building chain proxies: 3.61, per 1000 atoms: 0.62 Number of scatterers: 5828 At special positions: 0 Unit cell: (78.2, 103.5, 79.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 7 15.00 Mg 2 11.99 O 1075 8.00 N 1035 7.00 C 3676 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: 1.47 Conformation dependent library (CDL) restraints added in 856.2 milliseconds 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 10 sheets defined 32.1% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 267 through 277 removed outlier: 4.030A pdb=" N GLU A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 330 through 347 removed outlier: 4.452A pdb=" N GLN A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 removed outlier: 4.100A pdb=" N GLU A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 474 Processing helix chain 'A' and resid 528 through 539 removed outlier: 4.204A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N HIS A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 557 removed outlier: 3.646A pdb=" N GLU A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 removed outlier: 3.691A pdb=" N LEU A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.668A pdb=" N LYS A 611 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 631 through 650 removed outlier: 3.795A pdb=" N LYS A 644 " --> pdb=" O ASN A 640 " (cutoff:3.500A) Proline residue: A 647 - end of helix Processing helix chain 'A' and resid 665 through 675 removed outlier: 3.542A pdb=" N TYR A 669 " --> pdb=" O ARG A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 705 removed outlier: 3.835A pdb=" N LEU A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 725 through 740 removed outlier: 3.805A pdb=" N LEU A 734 " --> pdb=" O GLN A 730 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 735 " --> pdb=" O LYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 819 removed outlier: 3.656A pdb=" N LEU A 805 " --> pdb=" O HIS A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 852 removed outlier: 5.836A pdb=" N VAL A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Proline residue: A 846 - end of helix removed outlier: 3.828A pdb=" N PHE A 852 " --> pdb=" O PHE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 930 through 941 Processing helix chain 'A' and resid 955 through 971 Processing helix chain 'A' and resid 977 through 981 removed outlier: 3.532A pdb=" N SER A 981 " --> pdb=" O HIS A 978 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 786 through 791 removed outlier: 3.605A pdb=" N ALA A 773 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 772 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 760 " --> pdb=" O GLY A 774 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL A 756 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU A 863 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASP A 925 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL A 865 " --> pdb=" O ILE A 923 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 891 " --> pdb=" O VAL A 906 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 240 " --> pdb=" O MET A 580 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 247 removed outlier: 4.781A pdb=" N LEU A 387 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 388 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A 381 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 355 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 247 removed outlier: 4.781A pdb=" N LEU A 387 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 388 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A 381 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 372 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.621A pdb=" N ASP A 325 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 308 Processing sheet with id=AA6, first strand: chain 'A' and resid 432 through 433 Processing sheet with id=AA7, first strand: chain 'A' and resid 454 through 457 removed outlier: 3.548A pdb=" N ILE A 463 " --> pdb=" O PHE A 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA9, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AB1, first strand: chain 'A' and resid 657 through 660 removed outlier: 5.402A pdb=" N VAL A 625 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 624 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL A 687 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU A 626 " --> pdb=" O VAL A 687 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 621 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 937 1.32 - 1.44: 1594 1.44 - 1.57: 3365 1.57 - 1.69: 12 1.69 - 1.82: 54 Bond restraints: 5962 Sorted by residual: bond pdb=" C5 OMC B 25 " pdb=" C6 OMC B 25 " ideal model delta sigma weight residual 1.346 1.483 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C2 OMC B 25 " pdb=" N3 OMC B 25 " ideal model delta sigma weight residual 1.350 1.484 -0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" N3 OMC B 25 " pdb=" C4 OMC B 25 " ideal model delta sigma weight residual 1.317 1.448 -0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C4 OMC B 25 " pdb=" N4 OMC B 25 " ideal model delta sigma weight residual 1.332 1.436 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" N1 OMC B 25 " pdb=" C6 OMC B 25 " ideal model delta sigma weight residual 1.357 1.448 -0.091 2.00e-02 2.50e+03 2.08e+01 ... (remaining 5957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 7645 1.51 - 3.02: 385 3.02 - 4.53: 65 4.53 - 6.04: 14 6.04 - 7.55: 3 Bond angle restraints: 8112 Sorted by residual: angle pdb=" N GLN A 721 " pdb=" CA GLN A 721 " pdb=" C GLN A 721 " ideal model delta sigma weight residual 113.23 108.30 4.93 1.22e+00 6.72e-01 1.63e+01 angle pdb=" CA LYS A 899 " pdb=" C LYS A 899 " pdb=" O LYS A 899 " ideal model delta sigma weight residual 121.44 117.00 4.44 1.17e+00 7.31e-01 1.44e+01 angle pdb=" CA ILE A 299 " pdb=" C ILE A 299 " pdb=" O ILE A 299 " ideal model delta sigma weight residual 122.13 118.05 4.08 1.11e+00 8.12e-01 1.35e+01 angle pdb=" N GLN A 722 " pdb=" CA GLN A 722 " pdb=" C GLN A 722 " ideal model delta sigma weight residual 112.72 108.37 4.35 1.28e+00 6.10e-01 1.16e+01 angle pdb=" CA ASP A 902 " pdb=" C ASP A 902 " pdb=" O ASP A 902 " ideal model delta sigma weight residual 121.44 117.52 3.92 1.17e+00 7.31e-01 1.12e+01 ... (remaining 8107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 3276 17.39 - 34.78: 281 34.78 - 52.16: 38 52.16 - 69.55: 14 69.55 - 86.94: 10 Dihedral angle restraints: 3619 sinusoidal: 1477 harmonic: 2142 Sorted by residual: dihedral pdb=" CA ASN A 262 " pdb=" C ASN A 262 " pdb=" N PRO A 263 " pdb=" CA PRO A 263 " ideal model delta harmonic sigma weight residual 180.00 154.70 25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ASP A 325 " pdb=" C ASP A 325 " pdb=" N SER A 326 " pdb=" CA SER A 326 " ideal model delta harmonic sigma weight residual 180.00 157.10 22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA PRO A 512 " pdb=" C PRO A 512 " pdb=" N GLU A 513 " pdb=" CA GLU A 513 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 3616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 714 0.058 - 0.116: 182 0.116 - 0.174: 17 0.174 - 0.232: 5 0.232 - 0.290: 3 Chirality restraints: 921 Sorted by residual: chirality pdb=" CA ILE A 897 " pdb=" N ILE A 897 " pdb=" C ILE A 897 " pdb=" CB ILE A 897 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA ILE A 719 " pdb=" N ILE A 719 " pdb=" C ILE A 719 " pdb=" CB ILE A 719 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ASN A 262 " pdb=" N ASN A 262 " pdb=" C ASN A 262 " pdb=" CB ASN A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 918 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 522 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C ASP A 522 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP A 522 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A 523 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 647 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 648 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 648 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 648 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 859 " -0.016 2.00e-02 2.50e+03 1.35e-02 3.65e+00 pdb=" CG TYR A 859 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 859 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 859 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 859 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 859 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 859 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 859 " -0.001 2.00e-02 2.50e+03 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 60 2.54 - 3.13: 4690 3.13 - 3.72: 8780 3.72 - 4.31: 11862 4.31 - 4.90: 20306 Nonbonded interactions: 45698 Sorted by model distance: nonbonded pdb=" OP1 U B 3 " pdb="MG MG A1001 " model vdw 1.953 2.170 nonbonded pdb=" OXT LEU A 987 " pdb="MG MG A1001 " model vdw 1.963 2.170 nonbonded pdb=" O LEU A 987 " pdb="MG MG A1001 " model vdw 1.997 2.170 nonbonded pdb=" NH2 ARG A 583 " pdb=" OE1 GLN A 935 " model vdw 2.201 3.120 nonbonded pdb=" OE1 GLU A 364 " pdb=" NE2 GLN A 371 " model vdw 2.221 3.120 ... (remaining 45693 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 group one per residue 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: 0.050 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.270 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.007 0.137 5962 Z= 0.490 Angle : 0.786 7.550 8112 Z= 0.464 Chirality : 0.052 0.290 921 Planarity : 0.004 0.050 1018 Dihedral : 13.856 86.937 2231 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.17 % Allowed : 0.67 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.31), residues: 721 helix: -0.03 (0.38), residues: 199 sheet: -2.35 (0.41), residues: 147 loop : -2.50 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 373 HIS 0.006 0.001 HIS A 909 PHE 0.013 0.002 PHE A 852 TYR 0.032 0.002 TYR A 859 ARG 0.008 0.001 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 517 MET cc_start: 0.7805 (mpp) cc_final: 0.7497 (mpp) REVERT: A 743 GLU cc_start: 0.8404 (pm20) cc_final: 0.7992 (pt0) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.2008 time to fit residues: 22.5404 Evaluate side-chains 68 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN A 712 GLN A 722 GLN A 735 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN A 959 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.118931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.090506 restraints weight = 10704.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.090108 restraints weight = 7676.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.091930 restraints weight = 6702.733| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 5962 Z= 0.380 Angle : 0.649 7.812 8112 Z= 0.338 Chirality : 0.048 0.251 921 Planarity : 0.005 0.046 1018 Dihedral : 9.071 73.802 894 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 1.68 % Allowed : 10.07 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.31), residues: 721 helix: 0.52 (0.38), residues: 203 sheet: -2.30 (0.39), residues: 143 loop : -2.46 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 373 HIS 0.006 0.001 HIS A 909 PHE 0.028 0.002 PHE A 528 TYR 0.027 0.002 TYR A 859 ARG 0.003 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.571 Fit side-chains REVERT: A 517 MET cc_start: 0.7790 (mpp) cc_final: 0.7546 (mpp) REVERT: A 680 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6947 (tmm160) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.1603 time to fit residues: 17.7682 Evaluate side-chains 72 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 693 ASP Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 959 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.091436 restraints weight = 10683.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.091819 restraints weight = 7309.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.092755 restraints weight = 5928.570| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5962 Z= 0.247 Angle : 0.576 9.511 8112 Z= 0.298 Chirality : 0.045 0.209 921 Planarity : 0.004 0.049 1018 Dihedral : 8.861 73.642 894 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.01 % Allowed : 11.91 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.32), residues: 721 helix: 0.94 (0.39), residues: 200 sheet: -2.15 (0.39), residues: 140 loop : -2.32 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 623 HIS 0.005 0.001 HIS A 909 PHE 0.029 0.002 PHE A 528 TYR 0.020 0.002 TYR A 859 ARG 0.002 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.753 Fit side-chains REVERT: A 465 PHE cc_start: 0.8732 (m-80) cc_final: 0.8340 (m-80) REVERT: A 517 MET cc_start: 0.7705 (mpp) cc_final: 0.7490 (mpp) REVERT: A 573 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8105 (mp) REVERT: A 680 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7027 (tmm160) outliers start: 12 outliers final: 2 residues processed: 75 average time/residue: 0.1569 time to fit residues: 16.5844 Evaluate side-chains 71 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 680 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 18 optimal weight: 30.0000 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.121369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.092818 restraints weight = 10899.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.093277 restraints weight = 7267.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.094504 restraints weight = 5933.057| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5962 Z= 0.216 Angle : 0.552 7.680 8112 Z= 0.285 Chirality : 0.044 0.184 921 Planarity : 0.004 0.047 1018 Dihedral : 8.677 73.598 894 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.68 % Allowed : 13.26 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.32), residues: 721 helix: 1.20 (0.40), residues: 196 sheet: -2.07 (0.39), residues: 140 loop : -2.14 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 623 HIS 0.004 0.001 HIS A 909 PHE 0.016 0.002 PHE A 406 TYR 0.017 0.001 TYR A 244 ARG 0.003 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.626 Fit side-chains REVERT: A 465 PHE cc_start: 0.8642 (m-80) cc_final: 0.8234 (m-80) outliers start: 10 outliers final: 3 residues processed: 80 average time/residue: 0.1470 time to fit residues: 16.4947 Evaluate side-chains 74 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 761 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 56 optimal weight: 0.0670 chunk 10 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 overall best weight: 2.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.122354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.094093 restraints weight = 10585.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094976 restraints weight = 6863.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.096669 restraints weight = 5724.543| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5962 Z= 0.205 Angle : 0.557 9.768 8112 Z= 0.285 Chirality : 0.044 0.177 921 Planarity : 0.004 0.048 1018 Dihedral : 8.550 73.567 894 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.85 % Allowed : 14.77 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.32), residues: 721 helix: 1.23 (0.39), residues: 199 sheet: -2.20 (0.39), residues: 131 loop : -1.99 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 605 HIS 0.009 0.001 HIS A 368 PHE 0.015 0.002 PHE A 406 TYR 0.020 0.002 TYR A 859 ARG 0.003 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8680 (m-80) cc_final: 0.8216 (m-80) outliers start: 11 outliers final: 10 residues processed: 80 average time/residue: 0.1631 time to fit residues: 18.0343 Evaluate side-chains 80 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 959 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 68 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 67 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 HIS A 959 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.092291 restraints weight = 10681.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.093183 restraints weight = 6995.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.095427 restraints weight = 5395.259| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5962 Z= 0.310 Angle : 0.602 15.239 8112 Z= 0.301 Chirality : 0.045 0.174 921 Planarity : 0.004 0.045 1018 Dihedral : 8.558 73.738 894 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.35 % Allowed : 15.27 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.32), residues: 721 helix: 1.21 (0.39), residues: 199 sheet: -2.30 (0.39), residues: 135 loop : -1.97 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 605 HIS 0.005 0.001 HIS A 368 PHE 0.020 0.002 PHE A 852 TYR 0.022 0.002 TYR A 859 ARG 0.004 0.000 ARG A 921 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8678 (m-80) cc_final: 0.8207 (m-80) REVERT: A 658 MET cc_start: 0.8570 (tpp) cc_final: 0.8284 (tmm) REVERT: A 792 MET cc_start: 0.7310 (mmm) cc_final: 0.7003 (mmm) outliers start: 14 outliers final: 13 residues processed: 81 average time/residue: 0.1601 time to fit residues: 18.0214 Evaluate side-chains 83 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 959 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 51 optimal weight: 30.0000 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092515 restraints weight = 10734.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.093421 restraints weight = 7076.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.095796 restraints weight = 5445.259| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5962 Z= 0.270 Angle : 0.592 13.885 8112 Z= 0.296 Chirality : 0.044 0.168 921 Planarity : 0.004 0.046 1018 Dihedral : 8.552 73.682 894 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.68 % Allowed : 15.27 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.32), residues: 721 helix: 1.23 (0.39), residues: 199 sheet: -2.23 (0.40), residues: 137 loop : -1.94 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 623 HIS 0.004 0.001 HIS A 368 PHE 0.030 0.002 PHE A 852 TYR 0.019 0.002 TYR A 859 ARG 0.007 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8688 (m-80) cc_final: 0.8178 (m-80) REVERT: A 658 MET cc_start: 0.8574 (tpp) cc_final: 0.8327 (tmm) REVERT: A 792 MET cc_start: 0.7303 (mmm) cc_final: 0.6963 (mmm) REVERT: A 959 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8499 (m110) outliers start: 16 outliers final: 12 residues processed: 82 average time/residue: 0.1528 time to fit residues: 17.3404 Evaluate side-chains 84 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 959 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.091477 restraints weight = 10635.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.091752 restraints weight = 7456.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.093233 restraints weight = 6423.099| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5962 Z= 0.304 Angle : 0.599 12.812 8112 Z= 0.302 Chirality : 0.045 0.167 921 Planarity : 0.004 0.045 1018 Dihedral : 8.563 73.733 894 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.35 % Allowed : 15.60 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.32), residues: 721 helix: 1.29 (0.39), residues: 196 sheet: -2.28 (0.40), residues: 137 loop : -1.89 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 623 HIS 0.004 0.001 HIS A 909 PHE 0.021 0.002 PHE A 852 TYR 0.015 0.002 TYR A 244 ARG 0.007 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8668 (m-80) cc_final: 0.8160 (m-80) REVERT: A 658 MET cc_start: 0.8524 (tpp) cc_final: 0.8287 (tmm) REVERT: A 792 MET cc_start: 0.7352 (mmm) cc_final: 0.7011 (mmm) outliers start: 14 outliers final: 14 residues processed: 81 average time/residue: 0.1547 time to fit residues: 17.3800 Evaluate side-chains 84 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 959 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 30.0000 chunk 71 optimal weight: 0.0870 chunk 45 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 51 optimal weight: 30.0000 chunk 66 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.121470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.092590 restraints weight = 10736.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.093240 restraints weight = 7179.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094524 restraints weight = 5916.360| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5962 Z= 0.241 Angle : 0.594 13.435 8112 Z= 0.296 Chirality : 0.044 0.164 921 Planarity : 0.004 0.046 1018 Dihedral : 8.531 73.638 894 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.52 % Allowed : 15.44 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.33), residues: 721 helix: 1.33 (0.39), residues: 196 sheet: -2.17 (0.42), residues: 127 loop : -1.92 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 623 HIS 0.004 0.001 HIS A 368 PHE 0.013 0.001 PHE A 406 TYR 0.016 0.001 TYR A 244 ARG 0.007 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8702 (m-80) cc_final: 0.8148 (m-80) REVERT: A 792 MET cc_start: 0.7278 (mmm) cc_final: 0.6940 (mmm) REVERT: A 959 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8499 (m110) outliers start: 15 outliers final: 12 residues processed: 83 average time/residue: 0.1500 time to fit residues: 17.5677 Evaluate side-chains 85 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 959 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 52 optimal weight: 0.0980 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 18 optimal weight: 0.0980 chunk 7 optimal weight: 0.0030 chunk 50 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN A 959 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094133 restraints weight = 10481.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096854 restraints weight = 6465.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098644 restraints weight = 4774.277| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5962 Z= 0.146 Angle : 0.568 13.437 8112 Z= 0.282 Chirality : 0.044 0.160 921 Planarity : 0.004 0.049 1018 Dihedral : 8.359 73.419 894 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.34 % Allowed : 16.95 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.32), residues: 721 helix: 1.42 (0.39), residues: 199 sheet: -1.91 (0.43), residues: 125 loop : -1.96 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 623 HIS 0.004 0.000 HIS A 368 PHE 0.014 0.001 PHE A 406 TYR 0.015 0.001 TYR A 376 ARG 0.007 0.000 ARG A 354 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8562 (m-80) cc_final: 0.8015 (m-80) REVERT: A 792 MET cc_start: 0.7190 (mmm) cc_final: 0.6871 (mmm) outliers start: 8 outliers final: 3 residues processed: 80 average time/residue: 0.1711 time to fit residues: 18.8812 Evaluate side-chains 71 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 851 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 30.0000 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094531 restraints weight = 10634.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095587 restraints weight = 6932.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.097085 restraints weight = 5218.251| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5962 Z= 0.217 Angle : 0.569 13.290 8112 Z= 0.286 Chirality : 0.044 0.159 921 Planarity : 0.004 0.048 1018 Dihedral : 8.321 73.631 894 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.01 % Allowed : 17.79 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.33), residues: 721 helix: 1.46 (0.39), residues: 199 sheet: -1.90 (0.43), residues: 125 loop : -1.90 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 623 HIS 0.004 0.001 HIS A 909 PHE 0.030 0.002 PHE A 406 TYR 0.016 0.001 TYR A 244 ARG 0.007 0.000 ARG A 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1649.61 seconds wall clock time: 29 minutes 32.85 seconds (1772.85 seconds total)