Starting phenix.real_space_refine on Wed Mar 12 12:46:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w7t_32347/03_2025/7w7t_32347.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w7t_32347/03_2025/7w7t_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7w7t_32347/03_2025/7w7t_32347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w7t_32347/03_2025/7w7t_32347.map" model { file = "/net/cci-nas-00/data/ceres_data/7w7t_32347/03_2025/7w7t_32347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w7t_32347/03_2025/7w7t_32347.cif" } resolution = 3.4 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= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.02, per 1000 atoms: 0.64 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: 2.43 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.99 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: 3.11 Time building geometry restraints manager: 2.71 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.080 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 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 : 0.003 0.085 8049 Z= 0.192 Angle : 0.627 12.946 10924 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 : 10.32 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 (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: 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 TRP 0.017 0.001 TRP A 107 HIS 0.005 0.001 HIS A 526 PHE 0.029 0.001 PHE A 855 TYR 0.023 0.001 TYR A1030 ARG 0.009 0.000 ARG A 655 *********************** 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 : 0.811 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: 0.2044 time to fit residues: 36.5515 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 : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.0270 chunk 48 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 251 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** 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 = 0.4381 r_free = 0.4381 target = 0.209259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 126)---------------| | r_work = 0.4071 r_free = 0.4071 target = 0.176758 restraints weight = 8804.916| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.41 r_work: 0.3913 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8049 Z= 0.195 Angle : 0.578 5.917 10924 Z= 0.302 Chirality : 0.044 0.196 1282 Planarity : 0.004 0.046 1392 Dihedral : 4.267 18.239 1081 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.14 % Allowed : 7.31 % Favored : 91.54 % 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: 0.43 (0.26), residues: 1017 helix: 1.51 (0.23), residues: 504 sheet: 0.11 (0.66), residues: 68 loop : -1.14 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 272 HIS 0.003 0.001 HIS A 284 PHE 0.016 0.001 PHE A 855 TYR 0.015 0.001 TYR A 842 ARG 0.004 0.000 ARG A 559 *********************** 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 124 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.838 Fit side-chains REVERT: A 109 GLU cc_start: 0.7277 (tt0) cc_final: 0.7010 (tt0) REVERT: A 239 MET cc_start: 0.5451 (mpp) cc_final: 0.4580 (ttt) REVERT: A 453 ASN cc_start: 0.3683 (m110) cc_final: 0.3219 (t0) REVERT: A 566 HIS cc_start: 0.5490 (t70) cc_final: 0.5180 (t-170) REVERT: A 622 MET cc_start: 0.7995 (ttm) cc_final: 0.7783 (ttm) REVERT: A 699 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.6502 (ttt) REVERT: A 737 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7103 (m-30) REVERT: A 940 MET cc_start: 0.7461 (mmm) cc_final: 0.6650 (mmt) outliers start: 10 outliers final: 6 residues processed: 119 average time/residue: 0.2315 time to fit residues: 36.7712 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 : 0.899 ------------------------------------------------------------------------------- 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 699 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 916 SER Chi-restraints excluded: chain A residue 933 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 7 optimal weight: 0.0010 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A 790 GLN A 874 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.203063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.182346 restraints weight = 8792.461| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 0.80 r_work: 0.3870 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8049 Z= 0.254 Angle : 0.607 6.677 10924 Z= 0.313 Chirality : 0.045 0.198 1282 Planarity : 0.004 0.051 1392 Dihedral : 4.449 20.297 1081 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.83 % Allowed : 11.20 % Favored : 86.97 % 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: 0.15 (0.26), residues: 1017 helix: 1.32 (0.23), residues: 499 sheet: -0.15 (0.63), residues: 68 loop : -1.27 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 272 HIS 0.005 0.001 HIS A 405 PHE 0.019 0.002 PHE A 367 TYR 0.015 0.002 TYR A 842 ARG 0.003 0.001 ARG A 572 *********************** 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 120 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.871 Fit side-chains REVERT: A 239 MET cc_start: 0.5426 (mpp) cc_final: 0.4295 (ttt) REVERT: A 521 ILE cc_start: 0.6215 (OUTLIER) cc_final: 0.5751 (tp) REVERT: A 737 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: A 940 MET cc_start: 0.7259 (mmm) cc_final: 0.6332 (mmt) outliers start: 16 outliers final: 10 residues processed: 115 average time/residue: 0.2253 time to fit residues: 34.7778 Evaluate side-chains 110 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 699 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 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 26 optimal weight: 1.9990 chunk 64 optimal weight: 0.0870 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4371 r_free = 0.4371 target = 0.208145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.186794 restraints weight = 8760.786| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 0.85 r_work: 0.3890 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8049 Z= 0.180 Angle : 0.550 6.130 10924 Z= 0.284 Chirality : 0.042 0.132 1282 Planarity : 0.004 0.050 1392 Dihedral : 4.345 19.912 1081 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.94 % Allowed : 14.17 % Favored : 83.89 % 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: 0.30 (0.26), residues: 1017 helix: 1.47 (0.23), residues: 499 sheet: -0.18 (0.64), residues: 68 loop : -1.24 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 272 HIS 0.006 0.001 HIS A 284 PHE 0.033 0.001 PHE A 367 TYR 0.011 0.001 TYR A 842 ARG 0.003 0.000 ARG A 467 *********************** 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 121 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.874 Fit side-chains REVERT: A 239 MET cc_start: 0.5324 (mpp) cc_final: 0.4275 (ttt) REVERT: A 737 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7340 (m-30) REVERT: A 940 MET cc_start: 0.7141 (mmm) cc_final: 0.6303 (mmt) outliers start: 17 outliers final: 9 residues processed: 114 average time/residue: 0.2157 time to fit residues: 33.0270 Evaluate side-chains 108 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 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 91 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4300 r_free = 0.4300 target = 0.200078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.178948 restraints weight = 8763.652| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 0.85 r_work: 0.3829 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8049 Z= 0.310 Angle : 0.646 6.660 10924 Z= 0.333 Chirality : 0.046 0.247 1282 Planarity : 0.005 0.048 1392 Dihedral : 4.690 21.736 1081 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.09 % Allowed : 15.66 % Favored : 81.26 % 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: -0.16 (0.26), residues: 1017 helix: 1.03 (0.23), residues: 496 sheet: -0.06 (0.63), residues: 74 loop : -1.42 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 272 HIS 0.005 0.001 HIS A 284 PHE 0.032 0.002 PHE A 367 TYR 0.017 0.002 TYR A 122 ARG 0.003 0.001 ARG A 467 *********************** 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 132 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.409 Fit side-chains REVERT: A 239 MET cc_start: 0.5472 (mpp) cc_final: 0.4366 (ttt) REVERT: A 521 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6384 (tp) REVERT: A 737 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: A 806 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8305 (tt) REVERT: A 940 MET cc_start: 0.7165 (mmm) cc_final: 0.6177 (mmt) outliers start: 27 outliers final: 17 residues processed: 124 average time/residue: 0.2124 time to fit residues: 36.7609 Evaluate side-chains 116 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 404 CYS Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 577 LEU 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 806 LEU Chi-restraints excluded: chain A residue 881 ASP 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 11 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 0.0470 chunk 100 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4359 r_free = 0.4359 target = 0.207246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.186738 restraints weight = 8755.956| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 0.91 r_work: 0.3872 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8049 Z= 0.177 Angle : 0.562 6.919 10924 Z= 0.287 Chirality : 0.042 0.147 1282 Planarity : 0.004 0.047 1392 Dihedral : 4.429 20.699 1081 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.71 % Allowed : 19.09 % Favored : 79.20 % 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: 0.14 (0.26), residues: 1017 helix: 1.38 (0.23), residues: 500 sheet: -0.39 (0.60), residues: 68 loop : -1.34 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 793 HIS 0.003 0.001 HIS A 284 PHE 0.027 0.001 PHE A 367 TYR 0.010 0.001 TYR A 842 ARG 0.003 0.000 ARG A 467 *********************** 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 119 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.867 Fit side-chains REVERT: A 79 GLU cc_start: 0.4141 (tm-30) cc_final: 0.3463 (pm20) REVERT: A 239 MET cc_start: 0.5480 (mpp) cc_final: 0.4391 (ttt) REVERT: A 452 MET cc_start: 0.6694 (mpp) cc_final: 0.6064 (mpp) REVERT: A 521 ILE cc_start: 0.6286 (OUTLIER) cc_final: 0.5865 (tp) REVERT: A 737 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: A 806 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8201 (tt) REVERT: A 877 GLU cc_start: 0.6031 (tm-30) cc_final: 0.5246 (mp0) REVERT: A 940 MET cc_start: 0.7146 (mmm) cc_final: 0.6384 (mmt) outliers start: 15 outliers final: 9 residues processed: 117 average time/residue: 0.2179 time to fit residues: 34.3149 Evaluate side-chains 112 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 271 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 577 LEU 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 806 LEU 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 30 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.0270 chunk 32 optimal weight: 4.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4338 r_free = 0.4338 target = 0.204347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.184158 restraints weight = 8694.012| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 0.84 r_work: 0.3898 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8049 Z= 0.189 Angle : 0.574 9.646 10924 Z= 0.290 Chirality : 0.043 0.226 1282 Planarity : 0.004 0.046 1392 Dihedral : 4.386 20.970 1081 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.29 % Allowed : 18.86 % Favored : 78.86 % 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: 0.15 (0.26), residues: 1017 helix: 1.38 (0.23), residues: 501 sheet: -0.44 (0.59), residues: 68 loop : -1.32 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 272 HIS 0.006 0.001 HIS A 284 PHE 0.023 0.001 PHE A 367 TYR 0.011 0.001 TYR A 842 ARG 0.002 0.000 ARG A 467 *********************** 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 120 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.852 Fit side-chains REVERT: A 79 GLU cc_start: 0.4242 (tm-30) cc_final: 0.3497 (pm20) REVERT: A 235 ILE cc_start: 0.6206 (OUTLIER) cc_final: 0.5949 (mp) REVERT: A 239 MET cc_start: 0.5557 (mpp) cc_final: 0.4391 (ttt) REVERT: A 452 MET cc_start: 0.6639 (mpp) cc_final: 0.5989 (mpp) REVERT: A 521 ILE cc_start: 0.6677 (OUTLIER) cc_final: 0.6293 (tp) REVERT: A 737 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: A 806 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 877 GLU cc_start: 0.5740 (tm-30) cc_final: 0.5199 (mp0) REVERT: A 940 MET cc_start: 0.7119 (mmm) cc_final: 0.6393 (mmt) outliers start: 20 outliers final: 14 residues processed: 117 average time/residue: 0.2133 time to fit residues: 34.1123 Evaluate side-chains 117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 232 ILE Chi-restraints excluded: chain A residue 235 ILE 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 404 CYS Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 577 LEU 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 797 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4360 r_free = 0.4360 target = 0.207393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.185616 restraints weight = 8845.057| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 0.88 r_work: 0.3881 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8049 Z= 0.188 Angle : 0.569 9.079 10924 Z= 0.286 Chirality : 0.042 0.132 1282 Planarity : 0.004 0.044 1392 Dihedral : 4.351 20.902 1081 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.74 % Allowed : 18.63 % Favored : 78.63 % 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: 0.14 (0.26), residues: 1017 helix: 1.40 (0.23), residues: 502 sheet: -0.41 (0.59), residues: 68 loop : -1.38 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 272 HIS 0.007 0.001 HIS A 284 PHE 0.020 0.001 PHE A 367 TYR 0.011 0.001 TYR A 842 ARG 0.002 0.000 ARG A 636 *********************** 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 124 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.953 Fit side-chains REVERT: A 79 GLU cc_start: 0.4298 (tm-30) cc_final: 0.3562 (pm20) REVERT: A 235 ILE cc_start: 0.6255 (OUTLIER) cc_final: 0.5988 (mp) REVERT: A 239 MET cc_start: 0.5563 (mpp) cc_final: 0.4407 (ttt) REVERT: A 452 MET cc_start: 0.6624 (mpp) cc_final: 0.5978 (mpp) REVERT: A 478 LEU cc_start: 0.7009 (mt) cc_final: 0.6667 (pp) REVERT: A 521 ILE cc_start: 0.6366 (OUTLIER) cc_final: 0.6003 (tp) REVERT: A 737 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7613 (m-30) REVERT: A 794 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8327 (t) REVERT: A 806 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8205 (tt) REVERT: A 877 GLU cc_start: 0.5757 (tm-30) cc_final: 0.5223 (mp0) REVERT: A 940 MET cc_start: 0.7141 (mmm) cc_final: 0.6431 (mmt) outliers start: 24 outliers final: 16 residues processed: 121 average time/residue: 0.2171 time to fit residues: 36.4178 Evaluate side-chains 120 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 235 ILE 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 404 CYS Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 577 LEU 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 794 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 56 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 14 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 88 optimal weight: 0.0030 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4390 r_free = 0.4390 target = 0.210388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.189818 restraints weight = 8885.136| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 0.88 r_work: 0.3935 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8049 Z= 0.156 Angle : 0.564 9.123 10924 Z= 0.281 Chirality : 0.042 0.186 1282 Planarity : 0.004 0.044 1392 Dihedral : 4.228 19.996 1081 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.29 % Allowed : 19.66 % Favored : 78.06 % 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: 0.29 (0.26), residues: 1017 helix: 1.52 (0.23), residues: 501 sheet: -0.34 (0.60), residues: 68 loop : -1.29 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 793 HIS 0.007 0.001 HIS A 284 PHE 0.021 0.001 PHE A 367 TYR 0.008 0.001 TYR A 842 ARG 0.002 0.000 ARG A 164 *********************** 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 120 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.937 Fit side-chains REVERT: A 79 GLU cc_start: 0.4236 (tm-30) cc_final: 0.3539 (pm20) REVERT: A 235 ILE cc_start: 0.6316 (OUTLIER) cc_final: 0.6054 (mp) REVERT: A 239 MET cc_start: 0.5697 (mpp) cc_final: 0.4436 (ttt) REVERT: A 452 MET cc_start: 0.6475 (mpp) cc_final: 0.5841 (mpp) REVERT: A 478 LEU cc_start: 0.7012 (mt) cc_final: 0.6686 (pp) REVERT: A 521 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6301 (tp) REVERT: A 719 MET cc_start: 0.7778 (mtp) cc_final: 0.7303 (mmm) REVERT: A 737 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7191 (m-30) REVERT: A 767 ASN cc_start: 0.8018 (m-40) cc_final: 0.7725 (m-40) REVERT: A 794 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8284 (t) REVERT: A 877 GLU cc_start: 0.6104 (tm-30) cc_final: 0.5517 (mp0) REVERT: A 940 MET cc_start: 0.7102 (mmm) cc_final: 0.6481 (mmt) outliers start: 20 outliers final: 13 residues processed: 116 average time/residue: 0.2146 time to fit residues: 33.6318 Evaluate side-chains 115 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 235 ILE 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 577 LEU Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 794 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 39 optimal weight: 0.0570 chunk 65 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 99 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4412 r_free = 0.4412 target = 0.212651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.191475 restraints weight = 8767.833| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 0.87 r_work: 0.3938 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8049 Z= 0.147 Angle : 0.567 9.326 10924 Z= 0.281 Chirality : 0.042 0.141 1282 Planarity : 0.004 0.046 1392 Dihedral : 4.112 19.598 1081 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.71 % Allowed : 20.00 % Favored : 78.29 % 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: 0.42 (0.26), residues: 1017 helix: 1.62 (0.23), residues: 501 sheet: -0.33 (0.60), residues: 68 loop : -1.22 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 793 HIS 0.007 0.001 HIS A 284 PHE 0.021 0.001 PHE A 367 TYR 0.007 0.001 TYR A 842 ARG 0.006 0.000 ARG A 549 ********************** 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 115 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.889 Fit side-chains REVERT: A 16 PHE cc_start: 0.5849 (m-10) cc_final: 0.5648 (m-10) REVERT: A 79 GLU cc_start: 0.4179 (tm-30) cc_final: 0.3485 (pm20) REVERT: A 235 ILE cc_start: 0.6248 (OUTLIER) cc_final: 0.5972 (mp) REVERT: A 239 MET cc_start: 0.5566 (mpp) cc_final: 0.4404 (ttt) REVERT: A 252 LYS cc_start: 0.6928 (ptmt) cc_final: 0.6704 (ptpp) REVERT: A 452 MET cc_start: 0.6536 (mpp) cc_final: 0.5927 (mpp) REVERT: A 478 LEU cc_start: 0.6813 (mt) cc_final: 0.6585 (pp) REVERT: A 521 ILE cc_start: 0.6753 (OUTLIER) cc_final: 0.6332 (tp) REVERT: A 737 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: A 877 GLU cc_start: 0.6087 (tm-30) cc_final: 0.5531 (mp0) REVERT: A 940 MET cc_start: 0.7146 (mmm) cc_final: 0.6587 (mmt) outliers start: 15 outliers final: 11 residues processed: 112 average time/residue: 0.2106 time to fit residues: 32.3244 Evaluate side-chains 111 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 235 ILE 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 577 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.211489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.190136 restraints weight = 8801.698| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 0.89 r_work: 0.3983 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 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 0.036 8049 Z= 0.160 Angle : 0.570 10.015 10924 Z= 0.283 Chirality : 0.042 0.178 1282 Planarity : 0.004 0.049 1392 Dihedral : 4.089 18.709 1081 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.06 % Allowed : 20.34 % Favored : 77.60 % 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: 0.41 (0.26), residues: 1017 helix: 1.61 (0.23), residues: 501 sheet: -0.37 (0.60), residues: 68 loop : -1.21 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 854 HIS 0.007 0.001 HIS A 284 PHE 0.020 0.001 PHE A 367 TYR 0.009 0.001 TYR A 842 ARG 0.002 0.000 ARG A 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3726.74 seconds wall clock time: 65 minutes 26.30 seconds (3926.30 seconds total)