Starting phenix.real_space_refine on Thu Jul 2 08:29:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w7t_32347/07_2026/7w7t_32347.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w7t_32347/07_2026/7w7t_32347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7w7t_32347/07_2026/7w7t_32347.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w7t_32347/07_2026/7w7t_32347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w7t_32347/07_2026/7w7t_32347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w7t_32347/07_2026/7w7t_32347.map" model { file = "/net/cci-nas-00/data/ceres_data/7w7t_32347/07_2026/7w7t_32347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w7t_32347/07_2026/7w7t_32347.cif" } resolution = 3.4 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= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Mg 1 5.21 5 S 58 5.16 5 Be 1 3.05 5 C 5035 2.51 5 N 1318 2.21 5 O 1485 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7903 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 7896 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 46, 'TRANS': 974} Chain breaks: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 7 Unusual residues: {' CA': 2, ' MG': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.41, per 1000 atoms: 0.18 Number of scatterers: 7903 At special positions: 0 Unit cell: (103.335, 84.66, 138.195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 2 19.99 S 58 16.00 Mg 1 11.99 F 3 9.00 O 1485 8.00 N 1318 7.00 C 5035 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 875 " - pdb=" SG CYS A 887 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 331.0 milliseconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 54.4% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 removed outlier: 4.128A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 48 through 58 removed outlier: 4.188A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 76 Processing helix chain 'A' and resid 89 through 121 removed outlier: 3.749A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 226 through 229 Processing helix chain 'A' and resid 230 through 235 removed outlier: 4.097A pdb=" N ILE A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 247 through 276 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 287 through 306 Processing helix chain 'A' and resid 310 through 329 Processing helix chain 'A' and resid 335 through 344 removed outlier: 4.252A pdb=" N VAL A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.841A pdb=" N THR A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.787A pdb=" N ASP A 398 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP A 399 " --> pdb=" O HIS A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 395 through 399' Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 439 through 449 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 516 through 524 Processing helix chain 'A' and resid 537 through 552 Processing helix chain 'A' and resid 579 through 586 removed outlier: 3.669A pdb=" N PHE A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 617 removed outlier: 3.798A pdb=" N SER A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 672 Processing helix chain 'A' and resid 679 through 692 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.618A pdb=" N LYS A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'A' and resid 740 through 781 Processing helix chain 'A' and resid 787 through 800 Processing helix chain 'A' and resid 800 through 806 Processing helix chain 'A' and resid 807 through 809 No H-bonds generated for 'chain 'A' and resid 807 through 809' Processing helix chain 'A' and resid 814 through 818 removed outlier: 3.616A pdb=" N ASN A 817 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS A 818 " --> pdb=" O ILE A 815 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 814 through 818' Processing helix chain 'A' and resid 829 through 857 Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 888 through 891 Processing helix chain 'A' and resid 892 through 913 removed outlier: 4.361A pdb=" N MET A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 928 Processing helix chain 'A' and resid 929 through 948 Processing helix chain 'A' and resid 950 through 957 removed outlier: 4.493A pdb=" N LEU A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 955 " --> pdb=" O PRO A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 974 Processing helix chain 'A' and resid 974 through 990 removed outlier: 3.909A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1030 Proline residue: A1024 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 129 Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 153 removed outlier: 7.467A pdb=" N MET A 220 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.819A pdb=" N LEU A 173 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG A 174 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 332 through 333 removed outlier: 8.469A pdb=" N PHE A 675 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N MET A 622 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A 652 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 383 removed outlier: 5.832A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 495 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 369 through 372 removed outlier: 5.042A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 426 Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 529 418 hydrogen bonds defined for protein. 1206 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: 1.35 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2581 1.34 - 1.46: 1656 1.46 - 1.58: 3722 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 8049 Sorted by residual: bond pdb=" F2 BEF A4003 " pdb="BE BEF A4003 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" F3 BEF A4003 " pdb="BE BEF A4003 " ideal model delta sigma weight residual 1.476 1.547 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" F1 BEF A4003 " pdb="BE BEF A4003 " ideal model delta sigma weight residual 1.476 1.531 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" CB MET A 326 " pdb=" CG MET A 326 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.55e-01 bond pdb=" C GLU A 90 " pdb=" N PRO A 91 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.28e-02 6.10e+03 8.76e-01 ... (remaining 8044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 10821 2.59 - 5.18: 92 5.18 - 7.77: 8 7.77 - 10.36: 1 10.36 - 12.95: 2 Bond angle restraints: 10924 Sorted by residual: angle pdb=" N VAL A 647 " pdb=" CA VAL A 647 " pdb=" C VAL A 647 " ideal model delta sigma weight residual 111.91 107.93 3.98 8.90e-01 1.26e+00 2.00e+01 angle pdb=" F2 BEF A4003 " pdb="BE BEF A4003 " pdb=" F3 BEF A4003 " ideal model delta sigma weight residual 119.96 107.01 12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" F1 BEF A4003 " pdb="BE BEF A4003 " pdb=" F3 BEF A4003 " ideal model delta sigma weight residual 120.12 109.38 10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" N ASN A 403 " pdb=" CA ASN A 403 " pdb=" C ASN A 403 " ideal model delta sigma weight residual 114.04 109.89 4.15 1.24e+00 6.50e-01 1.12e+01 angle pdb=" C THR A 358 " pdb=" N ASN A 359 " pdb=" CA ASN A 359 " ideal model delta sigma weight residual 121.54 127.62 -6.08 1.91e+00 2.74e-01 1.01e+01 ... (remaining 10919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 4348 16.11 - 32.23: 416 32.23 - 48.34: 95 48.34 - 64.45: 14 64.45 - 80.56: 7 Dihedral angle restraints: 4880 sinusoidal: 1928 harmonic: 2952 Sorted by residual: dihedral pdb=" CG ARG A 655 " pdb=" CD ARG A 655 " pdb=" NE ARG A 655 " pdb=" CZ ARG A 655 " ideal model delta sinusoidal sigma weight residual 90.00 40.99 49.01 2 1.50e+01 4.44e-03 1.22e+01 dihedral pdb=" CA CYS A 887 " pdb=" C CYS A 887 " pdb=" N ALA A 888 " pdb=" CA ALA A 888 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASN A 421 " pdb=" CB ASN A 421 " pdb=" CG ASN A 421 " pdb=" OD1 ASN A 421 " ideal model delta sinusoidal sigma weight residual 120.00 -165.90 -74.10 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 4877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 829 0.034 - 0.068: 307 0.068 - 0.102: 109 0.102 - 0.136: 32 0.136 - 0.170: 5 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA GLU A 90 " pdb=" N GLU A 90 " pdb=" C GLU A 90 " pdb=" CB GLU A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CB VAL A 593 " pdb=" CA VAL A 593 " pdb=" CG1 VAL A 593 " pdb=" CG2 VAL A 593 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA VAL A 129 " pdb=" N VAL A 129 " pdb=" C VAL A 129 " pdb=" CB VAL A 129 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 1279 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 855 " 0.013 2.00e-02 2.50e+03 1.26e-02 2.76e+00 pdb=" CG PHE A 855 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 855 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 855 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 855 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 855 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 855 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 661 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A 662 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 662 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 662 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A1016 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A1017 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A1017 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1017 " -0.020 5.00e-02 4.00e+02 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 79 2.64 - 3.20: 7406 3.20 - 3.77: 12276 3.77 - 4.33: 16222 4.33 - 4.90: 27390 Nonbonded interactions: 63373 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A4004 " model vdw 2.069 2.170 nonbonded pdb=" O ASP A 351 " pdb=" OG1 THR A 355 " model vdw 2.076 3.040 nonbonded pdb=" O THR A 353 " pdb="MG MG A4004 " model vdw 2.084 2.170 nonbonded pdb=" F3 BEF A4003 " pdb="MG MG A4004 " model vdw 2.101 2.120 nonbonded pdb=" O ILE A 307 " pdb=" OE1 GLU A 309 " model vdw 2.149 3.040 ... (remaining 63368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.060 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 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 0.571 8051 Z= 0.652 Angle : 0.627 12.946 10926 Z= 0.336 Chirality : 0.042 0.170 1282 Planarity : 0.004 0.040 1392 Dihedral : 13.400 80.563 2963 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.11 % Allowed : 0.23 % Favored : 99.66 % 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 are not related in a simple way. whole: 0.71 (0.26), residues: 1017 helix: 1.84 (0.23), residues: 479 sheet: 0.19 (0.62), residues: 77 loop : -0.97 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 655 TYR 0.023 0.001 TYR A1030 PHE 0.029 0.001 PHE A 855 TRP 0.017 0.001 TRP A 107 HIS 0.005 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 8049) covalent geometry : angle 0.62715 / 0.34 (10924) SS BOND : bond 0.00056 / 0.03 ( 1) SS BOND : angle 1.03502 / 0.59 ( 2) hydrogen bonds : bond 0.16199 / 10.08 ( 418) hydrogen bonds : angle 6.17694 / 4.51 ( 1206) Misc. bond : bond 0.57061 / 30.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.168 Fit side-chains REVERT: A 239 MET cc_start: 0.5346 (mpp) cc_final: 0.4393 (ttt) REVERT: A 478 LEU cc_start: 0.6884 (pp) cc_final: 0.6572 (pp) REVERT: A 566 HIS cc_start: 0.5215 (t70) cc_final: 0.4776 (t-170) REVERT: A 622 MET cc_start: 0.7726 (ttm) cc_final: 0.7488 (ttm) REVERT: A 896 MET cc_start: 0.6916 (mtm) cc_final: 0.6618 (mtm) REVERT: A 940 MET cc_start: 0.7248 (mmm) cc_final: 0.6301 (mmt) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.0707 time to fit residues: 12.7584 Evaluate side-chains 103 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.0770 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN A 251 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.211271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 131)---------------| | r_work = 0.4128 r_free = 0.4128 target = 0.180846 restraints weight = 8856.881| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 1.24 r_work: 0.3789 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8051 Z= 0.123 Angle : 0.561 5.523 10926 Z= 0.292 Chirality : 0.043 0.191 1282 Planarity : 0.004 0.046 1392 Dihedral : 4.203 17.685 1081 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.14 % Allowed : 7.20 % Favored : 91.66 % 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 are not related in a simple way. whole: 0.54 (0.26), residues: 1017 helix: 1.60 (0.23), residues: 505 sheet: 0.14 (0.66), residues: 68 loop : -1.10 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 559 TYR 0.014 0.001 TYR A 842 PHE 0.015 0.001 PHE A 855 TRP 0.014 0.001 TRP A 272 HIS 0.003 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8049) covalent geometry : angle 0.56135 / 0.29 (10924) SS BOND : bond 0.00090 / 0.05 ( 1) SS BOND : angle 1.07769 / 0.60 ( 2) hydrogen bonds : bond 0.04638 / 3.15 ( 418) hydrogen bonds : angle 4.80334 / 3.48 ( 1206) Misc. bond : bond 0.00175 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.196 Fit side-chains REVERT: A 109 GLU cc_start: 0.7148 (tt0) cc_final: 0.6878 (tt0) REVERT: A 239 MET cc_start: 0.5399 (mpp) cc_final: 0.4545 (ttt) REVERT: A 453 ASN cc_start: 0.3549 (m110) cc_final: 0.3260 (t0) REVERT: A 566 HIS cc_start: 0.5514 (t70) cc_final: 0.5184 (t-170) REVERT: A 737 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: A 940 MET cc_start: 0.7333 (mmm) cc_final: 0.6559 (mmt) outliers start: 10 outliers final: 5 residues processed: 121 average time/residue: 0.0781 time to fit residues: 12.7551 Evaluate side-chains 107 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 59 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 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 = 0.4349 r_free = 0.4349 target = 0.205673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.4095 r_free = 0.4095 target = 0.177773 restraints weight = 8806.157| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.10 r_work: 0.3810 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8051 Z= 0.167 Angle : 0.607 7.654 10926 Z= 0.312 Chirality : 0.045 0.217 1282 Planarity : 0.004 0.051 1392 Dihedral : 4.386 20.090 1081 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.71 % Allowed : 11.20 % Favored : 87.09 % 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 are not related in a simple way. whole: 0.22 (0.26), residues: 1017 helix: 1.41 (0.23), residues: 498 sheet: -0.32 (0.63), residues: 69 loop : -1.25 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 572 TYR 0.016 0.002 TYR A 842 PHE 0.018 0.002 PHE A 367 TRP 0.021 0.002 TRP A 272 HIS 0.004 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 8049) covalent geometry : angle 0.60644 / 0.31 (10924) SS BOND : bond 0.00048 / 0.03 ( 1) SS BOND : angle 1.37138 / 0.77 ( 2) hydrogen bonds : bond 0.04941 / 3.39 ( 418) hydrogen bonds : angle 4.73521 / 3.42 ( 1206) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.191 Fit side-chains REVERT: A 239 MET cc_start: 0.5470 (mpp) cc_final: 0.4415 (ttt) REVERT: A 521 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.6089 (tp) REVERT: A 575 MET cc_start: 0.4355 (tpt) cc_final: 0.3954 (tmm) REVERT: A 714 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: A 737 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: A 940 MET cc_start: 0.7251 (mmm) cc_final: 0.6320 (mmt) outliers start: 15 outliers final: 9 residues processed: 114 average time/residue: 0.0813 time to fit residues: 12.5269 Evaluate side-chains 111 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 933 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 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 = 0.4392 r_free = 0.4392 target = 0.210119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.189051 restraints weight = 8917.878| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 0.84 r_work: 0.3908 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8051 Z= 0.113 Angle : 0.531 6.282 10926 Z= 0.273 Chirality : 0.042 0.131 1282 Planarity : 0.004 0.051 1392 Dihedral : 4.196 18.994 1081 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.49 % Allowed : 13.37 % Favored : 85.14 % 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 are not related in a simple way. whole: 0.41 (0.26), residues: 1017 helix: 1.59 (0.23), residues: 499 sheet: -0.23 (0.62), residues: 68 loop : -1.21 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.010 0.001 TYR A 842 PHE 0.032 0.001 PHE A 367 TRP 0.011 0.001 TRP A 272 HIS 0.006 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 8049) covalent geometry : angle 0.53097 / 0.27 (10924) SS BOND : bond 0.00053 / 0.03 ( 1) SS BOND : angle 1.09331 / 0.60 ( 2) hydrogen bonds : bond 0.04208 / 2.91 ( 418) hydrogen bonds : angle 4.49729 / 3.24 ( 1206) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.274 Fit side-chains REVERT: A 239 MET cc_start: 0.5423 (mpp) cc_final: 0.4325 (ttt) REVERT: A 366 MET cc_start: 0.5341 (OUTLIER) cc_final: 0.4940 (ttm) REVERT: A 737 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: A 767 ASN cc_start: 0.7991 (m-40) cc_final: 0.7763 (m-40) REVERT: A 940 MET cc_start: 0.7168 (mmm) cc_final: 0.6413 (mmt) outliers start: 13 outliers final: 6 residues processed: 113 average time/residue: 0.0722 time to fit residues: 11.2189 Evaluate side-chains 106 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 GLN ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.196697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.175702 restraints weight = 8905.645| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 0.91 r_work: 0.3775 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8051 Z= 0.270 Angle : 0.743 7.443 10926 Z= 0.386 Chirality : 0.050 0.242 1282 Planarity : 0.005 0.049 1392 Dihedral : 5.005 22.438 1081 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.74 % Allowed : 15.89 % Favored : 81.37 % 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 are not related in a simple way. whole: -0.61 (0.25), residues: 1017 helix: 0.61 (0.22), residues: 497 sheet: -0.29 (0.62), residues: 74 loop : -1.60 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 614 TYR 0.024 0.003 TYR A 122 PHE 0.035 0.002 PHE A 367 TRP 0.035 0.002 TRP A 272 HIS 0.006 0.002 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.27 ( 8049) covalent geometry : angle 0.74276 / 0.39 (10924) SS BOND : bond 0.00065 / 0.03 ( 1) SS BOND : angle 1.62243 / 0.90 ( 2) hydrogen bonds : bond 0.06059 / 4.17 ( 418) hydrogen bonds : angle 5.10048 / 3.69 ( 1206) Misc. bond : bond 0.00165 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.5591 (mpp) cc_final: 0.4502 (ttt) REVERT: A 521 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6421 (tp) REVERT: A 737 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: A 940 MET cc_start: 0.7203 (mmm) cc_final: 0.6391 (mmt) outliers start: 24 outliers final: 14 residues processed: 122 average time/residue: 0.0761 time to fit residues: 13.0008 Evaluate side-chains 114 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 954 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 HIS A 477 GLN ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.206926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.185065 restraints weight = 8806.596| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 0.90 r_work: 0.3858 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8051 Z= 0.119 Angle : 0.562 6.461 10926 Z= 0.288 Chirality : 0.042 0.136 1282 Planarity : 0.004 0.046 1392 Dihedral : 4.501 21.457 1081 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.71 % Allowed : 18.63 % Favored : 79.66 % 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 are not related in a simple way. whole: 0.03 (0.26), residues: 1017 helix: 1.28 (0.23), residues: 500 sheet: -0.40 (0.62), residues: 68 loop : -1.39 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 559 TYR 0.009 0.001 TYR A 842 PHE 0.028 0.001 PHE A 367 TRP 0.013 0.001 TRP A 793 HIS 0.011 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 8049) covalent geometry : angle 0.56210 / 0.29 (10924) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 1.20694 / 0.66 ( 2) hydrogen bonds : bond 0.04350 / 3.03 ( 418) hydrogen bonds : angle 4.59680 / 3.32 ( 1206) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.179 Fit side-chains REVERT: A 79 GLU cc_start: 0.4190 (tm-30) cc_final: 0.3501 (pm20) REVERT: A 239 MET cc_start: 0.5559 (mpp) cc_final: 0.4425 (ttt) REVERT: A 452 MET cc_start: 0.6725 (mpp) cc_final: 0.6354 (mpp) REVERT: A 521 ILE cc_start: 0.6301 (OUTLIER) cc_final: 0.5918 (tp) REVERT: A 737 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7567 (m-30) REVERT: A 767 ASN cc_start: 0.8105 (m-40) cc_final: 0.7793 (m-40) REVERT: A 877 GLU cc_start: 0.6069 (tm-30) cc_final: 0.5258 (mp0) REVERT: A 940 MET cc_start: 0.7116 (mmm) cc_final: 0.6431 (mmt) outliers start: 15 outliers final: 7 residues processed: 119 average time/residue: 0.0728 time to fit residues: 11.8159 Evaluate side-chains 107 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 0.0050 chunk 43 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 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 = 0.4290 r_free = 0.4290 target = 0.199121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.178777 restraints weight = 8883.882| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 0.87 r_work: 0.3817 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8051 Z= 0.198 Angle : 0.658 9.625 10926 Z= 0.335 Chirality : 0.046 0.229 1282 Planarity : 0.005 0.046 1392 Dihedral : 4.729 22.236 1081 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.17 % Allowed : 19.09 % Favored : 78.74 % 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 are not related in a simple way. whole: -0.33 (0.25), residues: 1017 helix: 0.97 (0.23), residues: 496 sheet: -0.26 (0.63), residues: 74 loop : -1.62 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 636 TYR 0.015 0.002 TYR A 122 PHE 0.023 0.002 PHE A 367 TRP 0.021 0.002 TRP A 272 HIS 0.007 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 8049) covalent geometry : angle 0.65764 / 0.33 (10924) SS BOND : bond 0.00020 / 0.01 ( 1) SS BOND : angle 1.31510 / 0.73 ( 2) hydrogen bonds : bond 0.05110 / 3.54 ( 418) hydrogen bonds : angle 4.80394 / 3.47 ( 1206) Misc. bond : bond 0.00087 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.254 Fit side-chains REVERT: A 239 MET cc_start: 0.5864 (mpp) cc_final: 0.4661 (ttt) REVERT: A 452 MET cc_start: 0.6931 (mpp) cc_final: 0.6520 (mpp) REVERT: A 521 ILE cc_start: 0.6757 (OUTLIER) cc_final: 0.6386 (tp) REVERT: A 737 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7792 (m-30) REVERT: A 877 GLU cc_start: 0.6079 (tm-30) cc_final: 0.5258 (mp0) REVERT: A 940 MET cc_start: 0.7174 (mmm) cc_final: 0.6358 (mmt) outliers start: 19 outliers final: 12 residues processed: 113 average time/residue: 0.0762 time to fit residues: 11.6383 Evaluate side-chains 109 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 954 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 GLN ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 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 = 0.4330 r_free = 0.4330 target = 0.203445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.182150 restraints weight = 8816.101| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 0.87 r_work: 0.3873 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8051 Z= 0.125 Angle : 0.578 8.772 10926 Z= 0.292 Chirality : 0.043 0.135 1282 Planarity : 0.004 0.046 1392 Dihedral : 4.498 22.322 1081 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.94 % Allowed : 19.66 % Favored : 78.40 % 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 are not related in a simple way. whole: -0.04 (0.26), residues: 1017 helix: 1.25 (0.23), residues: 502 sheet: -0.55 (0.61), residues: 68 loop : -1.46 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 636 TYR 0.010 0.001 TYR A 842 PHE 0.024 0.001 PHE A 367 TRP 0.011 0.001 TRP A 793 HIS 0.003 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 8049) covalent geometry : angle 0.57737 / 0.29 (10924) SS BOND : bond 0.00024 / 0.01 ( 1) SS BOND : angle 1.09966 / 0.60 ( 2) hydrogen bonds : bond 0.04307 / 3.00 ( 418) hydrogen bonds : angle 4.59206 / 3.32 ( 1206) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.201 Fit side-chains REVERT: A 79 GLU cc_start: 0.4171 (tm-30) cc_final: 0.3603 (pm20) REVERT: A 239 MET cc_start: 0.5795 (mpp) cc_final: 0.4592 (ttt) REVERT: A 452 MET cc_start: 0.6728 (mpp) cc_final: 0.6291 (mpp) REVERT: A 521 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.6040 (tp) REVERT: A 737 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7700 (m-30) REVERT: A 877 GLU cc_start: 0.5765 (tm-30) cc_final: 0.5248 (mp0) REVERT: A 940 MET cc_start: 0.7040 (mmm) cc_final: 0.6307 (mmt) outliers start: 17 outliers final: 11 residues processed: 115 average time/residue: 0.0678 time to fit residues: 10.7958 Evaluate side-chains 110 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 954 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 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 = 0.4329 r_free = 0.4329 target = 0.203231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.182801 restraints weight = 8765.955| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 0.87 r_work: 0.3880 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8051 Z= 0.135 Angle : 0.597 8.757 10926 Z= 0.301 Chirality : 0.043 0.202 1282 Planarity : 0.004 0.046 1392 Dihedral : 4.492 22.592 1081 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.71 % Allowed : 20.46 % Favored : 77.83 % 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 are not related in a simple way. whole: -0.02 (0.26), residues: 1017 helix: 1.29 (0.23), residues: 502 sheet: -0.52 (0.61), residues: 68 loop : -1.48 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 636 TYR 0.011 0.001 TYR A 842 PHE 0.024 0.001 PHE A 367 TRP 0.011 0.001 TRP A 272 HIS 0.004 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 8049) covalent geometry : angle 0.59692 / 0.30 (10924) SS BOND : bond 0.00001 / 0.00 ( 1) SS BOND : angle 1.05303 / 0.58 ( 2) hydrogen bonds : bond 0.04342 / 3.02 ( 418) hydrogen bonds : angle 4.60383 / 3.32 ( 1206) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.178 Fit side-chains REVERT: A 239 MET cc_start: 0.5824 (mpp) cc_final: 0.4596 (ttt) REVERT: A 452 MET cc_start: 0.6705 (mpp) cc_final: 0.6100 (mpp) REVERT: A 521 ILE cc_start: 0.6682 (OUTLIER) cc_final: 0.6301 (tp) REVERT: A 736 ASP cc_start: 0.6958 (p0) cc_final: 0.6709 (p0) REVERT: A 737 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: A 877 GLU cc_start: 0.5719 (tm-30) cc_final: 0.5256 (mp0) REVERT: A 940 MET cc_start: 0.7047 (mmm) cc_final: 0.6295 (mmt) outliers start: 15 outliers final: 10 residues processed: 109 average time/residue: 0.0675 time to fit residues: 10.2006 Evaluate side-chains 107 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 954 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 0.3980 chunk 3 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 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 = 0.4376 r_free = 0.4376 target = 0.208971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.187768 restraints weight = 8743.939| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 0.86 r_work: 0.3911 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8051 Z= 0.114 Angle : 0.569 9.740 10926 Z= 0.286 Chirality : 0.042 0.212 1282 Planarity : 0.004 0.049 1392 Dihedral : 4.329 21.922 1081 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.49 % Allowed : 20.57 % Favored : 77.94 % 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 are not related in a simple way. whole: 0.14 (0.26), residues: 1017 helix: 1.46 (0.23), residues: 501 sheet: -0.52 (0.62), residues: 62 loop : -1.42 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 365 TYR 0.008 0.001 TYR A 842 PHE 0.022 0.001 PHE A 279 TRP 0.012 0.001 TRP A 793 HIS 0.002 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 8049) covalent geometry : angle 0.56903 / 0.29 (10924) SS BOND : bond 0.00025 / 0.01 ( 1) SS BOND : angle 0.91602 / 0.50 ( 2) hydrogen bonds : bond 0.03943 / 2.74 ( 418) hydrogen bonds : angle 4.48284 / 3.22 ( 1206) Misc. bond : bond 0.00001 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.242 Fit side-chains REVERT: A 239 MET cc_start: 0.5861 (mpp) cc_final: 0.4616 (ttt) REVERT: A 452 MET cc_start: 0.6569 (mpp) cc_final: 0.5966 (mpp) REVERT: A 521 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6307 (tp) REVERT: A 736 ASP cc_start: 0.6982 (p0) cc_final: 0.6742 (p0) REVERT: A 737 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: A 877 GLU cc_start: 0.6202 (tm-30) cc_final: 0.5631 (mp0) REVERT: A 940 MET cc_start: 0.7041 (mmm) cc_final: 0.6336 (mmt) outliers start: 13 outliers final: 10 residues processed: 114 average time/residue: 0.0819 time to fit residues: 12.6492 Evaluate side-chains 108 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 954 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 32 optimal weight: 0.1980 chunk 101 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 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 = 0.4381 r_free = 0.4381 target = 0.209401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.189147 restraints weight = 8798.763| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 0.87 r_work: 0.3934 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8051 Z= 0.112 Angle : 0.567 9.329 10926 Z= 0.286 Chirality : 0.042 0.195 1282 Planarity : 0.004 0.048 1392 Dihedral : 4.282 21.327 1081 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.83 % Allowed : 20.46 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 1017 helix: 1.48 (0.23), residues: 502 sheet: -0.43 (0.61), residues: 62 loop : -1.36 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 572 TYR 0.008 0.001 TYR A 842 PHE 0.021 0.001 PHE A 279 TRP 0.009 0.001 TRP A 793 HIS 0.003 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 8049) covalent geometry : angle 0.56731 / 0.29 (10924) SS BOND : bond 0.00010 / 0.01 ( 1) SS BOND : angle 0.87884 / 0.48 ( 2) hydrogen bonds : bond 0.03909 / 2.71 ( 418) hydrogen bonds : angle 4.45504 / 3.20 ( 1206) Misc. bond : bond 0.00015 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1414.08 seconds wall clock time: 25 minutes 6.44 seconds (1506.44 seconds total)