Starting phenix.real_space_refine on Tue Mar 3 18:11:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w7t_32347/03_2026/7w7t_32347.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w7t_32347/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7w7t_32347/03_2026/7w7t_32347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w7t_32347/03_2026/7w7t_32347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w7t_32347/03_2026/7w7t_32347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w7t_32347/03_2026/7w7t_32347.map" } 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-5986/lib/python3.9/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: 1.94, per 1000 atoms: 0.25 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: 0.91 Conformation dependent library (CDL) restraints added in 428.7 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: 0.26 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: 1.24 Time building geometry restraints manager: 1.17 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: 0.320 Set stop_for_unknowns flag: 0.010 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.410 Find NCS groups from input model: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.200 ------------------------------------------------------------------------------- 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 : 0.007 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 covalent geometry : bond 0.00292 ( 8049) covalent geometry : angle 0.62715 (10924) SS BOND : bond 0.00056 ( 1) SS BOND : angle 1.03502 ( 2) hydrogen bonds : bond 0.16199 ( 418) hydrogen bonds : angle 6.17694 ( 1206) Misc. bond : bond 0.57061 ( 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 : 0.277 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: 0.6300 (mmt) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.0882 time to fit residues: 15.9231 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 : 0.257 ------------------------------------------------------------------------------- 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: 6.9990 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... 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** 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 = 0.211264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.4156 r_free = 0.4156 target = 0.183986 restraints weight = 8856.358| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 1.10 r_work: 0.3885 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8051 Z= 0.122 Angle : 0.559 5.542 10926 Z= 0.291 Chirality : 0.043 0.189 1282 Planarity : 0.004 0.046 1392 Dihedral : 4.197 17.677 1081 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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 : -1.09 (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 0.015 0.001 TRP A 272 HIS 0.003 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8049) covalent geometry : angle 0.55922 (10924) SS BOND : bond 0.00079 ( 1) SS BOND : angle 1.07931 ( 2) hydrogen bonds : bond 0.04621 ( 418) hydrogen bonds : angle 4.79543 ( 1206) Misc. bond : bond 0.00144 ( 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 : 0.312 Fit side-chains REVERT: A 109 GLU cc_start: 0.7129 (tt0) cc_final: 0.6854 (tt0) REVERT: A 239 MET cc_start: 0.5400 (mpp) cc_final: 0.4496 (ttt) REVERT: A 566 HIS cc_start: 0.5532 (t70) cc_final: 0.5177 (t-170) REVERT: A 622 MET cc_start: 0.7919 (ttm) cc_final: 0.7705 (ttm) REVERT: A 737 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6956 (m-30) REVERT: A 940 MET cc_start: 0.7244 (mmm) cc_final: 0.6468 (mmt) outliers start: 10 outliers final: 5 residues processed: 121 average time/residue: 0.0980 time to fit residues: 15.8302 Evaluate side-chains 108 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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: 5.9990 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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** A 790 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.204671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.184030 restraints weight = 8806.504| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 0.86 r_work: 0.3877 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8051 Z= 0.194 Angle : 0.644 7.919 10926 Z= 0.332 Chirality : 0.046 0.205 1282 Planarity : 0.004 0.051 1392 Dihedral : 4.538 20.544 1081 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.83 % Allowed : 11.66 % Favored : 86.51 % 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: 0.05 (0.26), residues: 1017 helix: 1.23 (0.23), residues: 494 sheet: -0.05 (0.62), residues: 74 loop : -1.34 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 614 TYR 0.016 0.002 TYR A 122 PHE 0.021 0.002 PHE A 367 TRP 0.026 0.002 TRP A 272 HIS 0.004 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 8049) covalent geometry : angle 0.64346 (10924) SS BOND : bond 0.00042 ( 1) SS BOND : angle 1.51697 ( 2) hydrogen bonds : bond 0.05294 ( 418) hydrogen bonds : angle 4.83736 ( 1206) Misc. bond : bond 0.00097 ( 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 121 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.197 Fit side-chains REVERT: A 239 MET cc_start: 0.5415 (mpp) cc_final: 0.4279 (ttt) REVERT: A 521 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6228 (tp) REVERT: A 699 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.5779 (tpt) REVERT: A 714 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: A 737 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: A 940 MET cc_start: 0.7226 (mmm) cc_final: 0.6300 (mmt) outliers start: 16 outliers final: 9 residues processed: 116 average time/residue: 0.0874 time to fit residues: 13.8207 Evaluate side-chains 111 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 5 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 7 optimal weight: 0.0470 chunk 6 optimal weight: 3.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.207263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.186181 restraints weight = 8930.218| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 0.82 r_work: 0.3888 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.1962 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= 0.132 Angle : 0.559 6.174 10926 Z= 0.288 Chirality : 0.043 0.133 1282 Planarity : 0.004 0.050 1392 Dihedral : 4.374 20.015 1081 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.17 % Allowed : 14.17 % Favored : 83.66 % 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: 0.20 (0.26), residues: 1017 helix: 1.38 (0.23), residues: 499 sheet: -0.36 (0.62), residues: 68 loop : -1.24 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.011 0.001 TYR A 842 PHE 0.033 0.001 PHE A 367 TRP 0.014 0.001 TRP A 272 HIS 0.006 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8049) covalent geometry : angle 0.55896 (10924) SS BOND : bond 0.00074 ( 1) SS BOND : angle 1.21682 ( 2) hydrogen bonds : bond 0.04509 ( 418) hydrogen bonds : angle 4.59259 ( 1206) Misc. bond : bond 0.00048 ( 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 121 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.5341 (mpp) cc_final: 0.4237 (ttt) REVERT: A 737 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: A 940 MET cc_start: 0.7156 (mmm) cc_final: 0.6361 (mmt) outliers start: 19 outliers final: 11 residues processed: 115 average time/residue: 0.0990 time to fit residues: 15.3894 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 : 0.257 ------------------------------------------------------------------------------- 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 404 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.207338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.185563 restraints weight = 8827.980| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 0.89 r_work: 0.3868 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8051 Z= 0.133 Angle : 0.565 6.291 10926 Z= 0.289 Chirality : 0.043 0.229 1282 Planarity : 0.004 0.049 1392 Dihedral : 4.352 19.859 1081 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.06 % Allowed : 16.00 % Favored : 81.94 % 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: 0.22 (0.26), residues: 1017 helix: 1.40 (0.23), residues: 500 sheet: -0.43 (0.61), residues: 68 loop : -1.23 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.011 0.001 TYR A 842 PHE 0.028 0.001 PHE A 367 TRP 0.013 0.001 TRP A 272 HIS 0.006 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8049) covalent geometry : angle 0.56492 (10924) SS BOND : bond 0.00045 ( 1) SS BOND : angle 1.16328 ( 2) hydrogen bonds : bond 0.04435 ( 418) hydrogen bonds : angle 4.57262 ( 1206) Misc. bond : bond 0.00048 ( 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 119 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.271 Fit side-chains REVERT: A 239 MET cc_start: 0.5478 (mpp) cc_final: 0.4414 (ttt) REVERT: A 521 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6286 (tp) REVERT: A 737 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: A 767 ASN cc_start: 0.8086 (m-40) cc_final: 0.7780 (m-40) REVERT: A 806 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8232 (tt) REVERT: A 940 MET cc_start: 0.7219 (mmm) cc_final: 0.6489 (mmt) outliers start: 18 outliers final: 8 residues processed: 114 average time/residue: 0.0959 time to fit residues: 14.7507 Evaluate side-chains 110 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 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 806 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 916 SER 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: 7.9990 chunk 90 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 83 optimal weight: 0.0970 chunk 11 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.208921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.4186 r_free = 0.4186 target = 0.187596 restraints weight = 8784.269| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 0.86 r_work: 0.3898 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8051 Z= 0.116 Angle : 0.549 6.923 10926 Z= 0.277 Chirality : 0.042 0.131 1282 Planarity : 0.004 0.047 1392 Dihedral : 4.267 19.690 1081 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.83 % Allowed : 18.40 % Favored : 79.77 % 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: 0.35 (0.26), residues: 1017 helix: 1.53 (0.23), residues: 499 sheet: -0.37 (0.60), residues: 68 loop : -1.19 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 467 TYR 0.010 0.001 TYR A 842 PHE 0.026 0.001 PHE A 367 TRP 0.010 0.001 TRP A 272 HIS 0.006 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8049) covalent geometry : angle 0.54917 (10924) SS BOND : bond 0.00027 ( 1) SS BOND : angle 1.05746 ( 2) hydrogen bonds : bond 0.04111 ( 418) hydrogen bonds : angle 4.48960 ( 1206) Misc. bond : bond 0.00030 ( 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 120 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.304 Fit side-chains REVERT: A 239 MET cc_start: 0.5464 (mpp) cc_final: 0.4384 (ttt) REVERT: A 521 ILE cc_start: 0.6479 (OUTLIER) cc_final: 0.6083 (tp) REVERT: A 737 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: A 767 ASN cc_start: 0.8104 (m-40) cc_final: 0.7870 (m-40) REVERT: A 806 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8182 (tt) REVERT: A 877 GLU cc_start: 0.5884 (tm-30) cc_final: 0.5247 (mp0) REVERT: A 940 MET cc_start: 0.7197 (mmm) cc_final: 0.6508 (mmt) outliers start: 16 outliers final: 9 residues processed: 119 average time/residue: 0.0882 time to fit residues: 14.3418 Evaluate side-chains 113 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 289 ILE Chi-restraints excluded: chain A residue 321 LEU 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 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 15 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.4319 r_free = 0.4319 target = 0.202817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.181616 restraints weight = 8932.679| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 0.87 r_work: 0.3832 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8051 Z= 0.197 Angle : 0.652 9.949 10926 Z= 0.332 Chirality : 0.046 0.238 1282 Planarity : 0.004 0.046 1392 Dihedral : 4.638 21.154 1081 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.17 % Allowed : 18.74 % Favored : 79.09 % 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: -0.18 (0.25), residues: 1017 helix: 1.03 (0.23), residues: 502 sheet: -0.61 (0.58), residues: 69 loop : -1.40 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 636 TYR 0.016 0.002 TYR A 122 PHE 0.027 0.002 PHE A 367 TRP 0.025 0.002 TRP A 272 HIS 0.005 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8049) covalent geometry : angle 0.65193 (10924) SS BOND : bond 0.00012 ( 1) SS BOND : angle 1.30742 ( 2) hydrogen bonds : bond 0.05099 ( 418) hydrogen bonds : angle 4.76357 ( 1206) Misc. bond : bond 0.00081 ( 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 119 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.241 Fit side-chains REVERT: A 235 ILE cc_start: 0.6611 (OUTLIER) cc_final: 0.6404 (mp) REVERT: A 239 MET cc_start: 0.5659 (mpp) cc_final: 0.4515 (ttt) REVERT: A 521 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6329 (tp) REVERT: A 737 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: A 806 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8315 (tt) REVERT: A 877 GLU cc_start: 0.6055 (tm-30) cc_final: 0.5299 (mp0) REVERT: A 940 MET cc_start: 0.7183 (mmm) cc_final: 0.6365 (mmt) outliers start: 19 outliers final: 14 residues processed: 115 average time/residue: 0.0840 time to fit residues: 13.4550 Evaluate side-chains 116 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain A residue 933 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.207028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.185628 restraints weight = 8888.204| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 0.91 r_work: 0.3873 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2469 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= 0.123 Angle : 0.572 9.036 10926 Z= 0.289 Chirality : 0.042 0.132 1282 Planarity : 0.004 0.045 1392 Dihedral : 4.401 20.187 1081 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.17 % Allowed : 18.51 % Favored : 79.31 % 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: 0.11 (0.26), residues: 1017 helix: 1.35 (0.23), residues: 501 sheet: -0.45 (0.59), residues: 68 loop : -1.34 (0.28), residues: 448 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 0.025 0.001 PHE A 367 TRP 0.011 0.001 TRP A 793 HIS 0.004 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8049) covalent geometry : angle 0.57144 (10924) SS BOND : bond 0.00032 ( 1) SS BOND : angle 1.08095 ( 2) hydrogen bonds : bond 0.04277 ( 418) hydrogen bonds : angle 4.53274 ( 1206) Misc. bond : bond 0.00018 ( 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 125 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.276 Fit side-chains REVERT: A 79 GLU cc_start: 0.4151 (tm-30) cc_final: 0.3493 (pm20) REVERT: A 235 ILE cc_start: 0.6628 (OUTLIER) cc_final: 0.6376 (mp) REVERT: A 239 MET cc_start: 0.5699 (mpp) cc_final: 0.4473 (ttt) REVERT: A 521 ILE cc_start: 0.6394 (OUTLIER) cc_final: 0.5993 (tp) REVERT: A 551 TRP cc_start: 0.5593 (m-10) cc_final: 0.5391 (m-10) REVERT: A 719 MET cc_start: 0.7743 (mtp) cc_final: 0.7528 (mtp) REVERT: A 737 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7475 (m-30) REVERT: A 767 ASN cc_start: 0.8161 (m-40) cc_final: 0.7853 (m-40) REVERT: A 806 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8221 (tt) REVERT: A 877 GLU cc_start: 0.5768 (tm-30) cc_final: 0.5222 (mp0) REVERT: A 940 MET cc_start: 0.7103 (mmm) cc_final: 0.6420 (mmt) outliers start: 19 outliers final: 13 residues processed: 123 average time/residue: 0.0917 time to fit residues: 15.3793 Evaluate side-chains 117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 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 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: 0.7980 chunk 46 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.209917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.188520 restraints weight = 8782.136| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 0.87 r_work: 0.3909 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2487 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= 0.110 Angle : 0.578 9.112 10926 Z= 0.286 Chirality : 0.042 0.190 1282 Planarity : 0.004 0.046 1392 Dihedral : 4.252 19.895 1081 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.94 % Allowed : 19.43 % 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 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: 0.31 (0.26), residues: 1017 helix: 1.51 (0.23), residues: 501 sheet: -0.31 (0.59), residues: 68 loop : -1.26 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 164 TYR 0.008 0.001 TYR A 842 PHE 0.025 0.001 PHE A 367 TRP 0.010 0.001 TRP A 793 HIS 0.005 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8049) covalent geometry : angle 0.57816 (10924) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.87108 ( 2) hydrogen bonds : bond 0.03886 ( 418) hydrogen bonds : angle 4.45305 ( 1206) Misc. bond : bond 0.00003 ( 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 121 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.297 Fit side-chains REVERT: A 79 GLU cc_start: 0.4284 (tm-30) cc_final: 0.3562 (pm20) REVERT: A 235 ILE cc_start: 0.6299 (OUTLIER) cc_final: 0.6028 (mp) REVERT: A 239 MET cc_start: 0.5693 (mpp) cc_final: 0.4479 (ttt) REVERT: A 478 LEU cc_start: 0.6919 (mt) cc_final: 0.6620 (pp) REVERT: A 521 ILE cc_start: 0.6774 (OUTLIER) cc_final: 0.6286 (tp) REVERT: A 737 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: A 806 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8159 (tt) REVERT: A 877 GLU cc_start: 0.6161 (tm-30) cc_final: 0.5538 (mp0) REVERT: A 940 MET cc_start: 0.7153 (mmm) cc_final: 0.6572 (mmt) outliers start: 17 outliers final: 12 residues processed: 118 average time/residue: 0.0968 time to fit residues: 15.5576 Evaluate side-chains 113 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 92 optimal weight: 0.0010 chunk 94 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.1590 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.204835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.184560 restraints weight = 8810.085| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 0.86 r_work: 0.3872 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8051 Z= 0.173 Angle : 0.638 9.218 10926 Z= 0.319 Chirality : 0.044 0.167 1282 Planarity : 0.004 0.048 1392 Dihedral : 4.457 20.230 1081 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.17 % Allowed : 19.77 % 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 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: 1.23 (0.23), residues: 500 sheet: -0.60 (0.58), residues: 69 loop : -1.37 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 636 TYR 0.015 0.002 TYR A 842 PHE 0.016 0.002 PHE A 279 TRP 0.020 0.001 TRP A 272 HIS 0.007 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8049) covalent geometry : angle 0.63805 (10924) SS BOND : bond 0.00036 ( 1) SS BOND : angle 1.11503 ( 2) hydrogen bonds : bond 0.04637 ( 418) hydrogen bonds : angle 4.62888 ( 1206) Misc. bond : bond 0.00052 ( 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 118 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.310 Fit side-chains REVERT: A 235 ILE cc_start: 0.6402 (OUTLIER) cc_final: 0.6141 (mp) REVERT: A 239 MET cc_start: 0.5809 (mpp) cc_final: 0.4586 (ttt) REVERT: A 478 LEU cc_start: 0.6985 (mt) cc_final: 0.6702 (pp) REVERT: A 521 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6274 (tp) REVERT: A 736 ASP cc_start: 0.6882 (p0) cc_final: 0.6676 (p0) REVERT: A 737 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: A 806 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8270 (tt) REVERT: A 877 GLU cc_start: 0.5727 (tm-30) cc_final: 0.5226 (mp0) REVERT: A 940 MET cc_start: 0.7157 (mmm) cc_final: 0.6391 (mmt) outliers start: 19 outliers final: 15 residues processed: 116 average time/residue: 0.0946 time to fit residues: 14.9418 Evaluate side-chains 116 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 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 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: 10.0000 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 101 optimal weight: 0.0040 chunk 26 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.208072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.186239 restraints weight = 8790.908| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 0.90 r_work: 0.3879 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8051 Z= 0.118 Angle : 0.591 9.545 10926 Z= 0.293 Chirality : 0.043 0.204 1282 Planarity : 0.004 0.048 1392 Dihedral : 4.336 20.236 1081 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.40 % Allowed : 19.77 % 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: 0.17 (0.26), residues: 1017 helix: 1.41 (0.23), residues: 500 sheet: -0.41 (0.59), residues: 68 loop : -1.33 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 164 TYR 0.009 0.001 TYR A 842 PHE 0.024 0.001 PHE A 367 TRP 0.013 0.001 TRP A 551 HIS 0.006 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8049) covalent geometry : angle 0.59110 (10924) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.95035 ( 2) hydrogen bonds : bond 0.04100 ( 418) hydrogen bonds : angle 4.49020 ( 1206) Misc. bond : bond 0.00014 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1623.42 seconds wall clock time: 28 minutes 36.14 seconds (1716.14 seconds total)