Starting phenix.real_space_refine on Thu Sep 26 19:15:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w84_32351/09_2024/7w84_32351.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w84_32351/09_2024/7w84_32351.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w84_32351/09_2024/7w84_32351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w84_32351/09_2024/7w84_32351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w84_32351/09_2024/7w84_32351.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w84_32351/09_2024/7w84_32351.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= 0.184 sd= 0.712 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7474 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 4993 2.51 5 N 1376 2.21 5 O 1461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7879 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7879 Classifications: {'peptide': 995} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 949} Chain breaks: 1 Time building chain proxies: 5.08, per 1000 atoms: 0.64 Number of scatterers: 7879 At special positions: 0 Unit cell: (81.18, 104.28, 101.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1461 8.00 N 1376 7.00 C 4993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 805 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 867.0 milliseconds 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1874 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 8 sheets defined 40.1% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 229 through 234 removed outlier: 4.249A pdb=" N GLU A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 303 Processing helix chain 'A' and resid 312 through 322 removed outlier: 3.726A pdb=" N LEU A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.534A pdb=" N LEU A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 359 removed outlier: 3.502A pdb=" N ASN A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET A 357 " --> pdb=" O HIS A 353 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS A 359 " --> pdb=" O MET A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 401 removed outlier: 3.690A pdb=" N LYS A 399 " --> pdb=" O ASN A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 removed outlier: 3.717A pdb=" N LEU A 426 " --> pdb=" O PRO A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 441 through 453 removed outlier: 3.901A pdb=" N HIS A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 474 Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.570A pdb=" N GLY A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 554 through 564 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 640 through 658 removed outlier: 4.323A pdb=" N PHE A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 671 removed outlier: 3.965A pdb=" N LYS A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 693 through 715 Processing helix chain 'A' and resid 747 through 751 Processing helix chain 'A' and resid 794 through 800 Processing helix chain 'A' and resid 816 through 820 Processing helix chain 'A' and resid 862 through 877 removed outlier: 3.613A pdb=" N ILE A 866 " --> pdb=" O THR A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 892 Processing helix chain 'A' and resid 899 through 913 Processing helix chain 'A' and resid 914 through 916 No H-bonds generated for 'chain 'A' and resid 914 through 916' Processing helix chain 'A' and resid 934 through 938 removed outlier: 4.131A pdb=" N MET A 937 " --> pdb=" O PRO A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.944A pdb=" N GLU A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ARG A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1023 removed outlier: 3.800A pdb=" N ILE A1020 " --> pdb=" O ARG A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1034 removed outlier: 4.341A pdb=" N ARG A1034 " --> pdb=" O VAL A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1064 removed outlier: 3.614A pdb=" N CYS A1064 " --> pdb=" O TRP A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1067 No H-bonds generated for 'chain 'A' and resid 1065 through 1067' Processing helix chain 'A' and resid 1068 through 1082 removed outlier: 3.554A pdb=" N HIS A1082 " --> pdb=" O HIS A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1097 Processing helix chain 'A' and resid 1098 through 1103 Processing helix chain 'A' and resid 1103 through 1110 removed outlier: 3.636A pdb=" N ALA A1107 " --> pdb=" O LEU A1103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.699A pdb=" N ALA A 111 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 135 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA A 113 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ASP A 133 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU A 115 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER A 131 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 117 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY A 134 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LYS A 151 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 372 through 374 Processing sheet with id=AA3, first strand: chain 'A' and resid 384 through 386 removed outlier: 6.446A pdb=" N ILE A 377 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TRP A 478 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 536 through 538 Processing sheet with id=AA5, first strand: chain 'A' and resid 550 through 553 removed outlier: 6.196A pdb=" N GLY A 551 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 625 through 626 removed outlier: 3.609A pdb=" N VAL A 626 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE A 717 " --> pdb=" O VAL A 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 739 through 740 removed outlier: 8.531A pdb=" N VAL A 806 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE A 726 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE A 808 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N CYS A 728 " --> pdb=" O PHE A 808 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 744 through 745 removed outlier: 6.814A pdb=" N THR A 766 " --> pdb=" O ASP A 762 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP A 762 " --> pdb=" O THR A 766 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 768 " --> pdb=" O CYS A 760 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 855 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: 2.50 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2539 1.34 - 1.46: 1164 1.46 - 1.57: 4274 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 8052 Sorted by residual: bond pdb=" CA GLU A 252 " pdb=" C GLU A 252 " ideal model delta sigma weight residual 1.524 1.489 0.036 1.22e-02 6.72e+03 8.48e+00 bond pdb=" N ASN A1024 " pdb=" CA ASN A1024 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.21e-02 6.83e+03 7.56e+00 bond pdb=" N ASP A 964 " pdb=" CA ASP A 964 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.51e+00 bond pdb=" CA LEU A 362 " pdb=" C LEU A 362 " ideal model delta sigma weight residual 1.526 1.496 0.030 1.18e-02 7.18e+03 6.27e+00 bond pdb=" N SER A 602 " pdb=" CA SER A 602 " ideal model delta sigma weight residual 1.455 1.488 -0.034 1.37e-02 5.33e+03 6.01e+00 ... (remaining 8047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 10622 2.08 - 4.17: 230 4.17 - 6.25: 25 6.25 - 8.34: 4 8.34 - 10.42: 2 Bond angle restraints: 10883 Sorted by residual: angle pdb=" N ARG A 358 " pdb=" CA ARG A 358 " pdb=" C ARG A 358 " ideal model delta sigma weight residual 111.07 100.65 10.42 1.07e+00 8.73e-01 9.48e+01 angle pdb=" N LEU A 251 " pdb=" CA LEU A 251 " pdb=" C LEU A 251 " ideal model delta sigma weight residual 112.92 102.73 10.19 1.23e+00 6.61e-01 6.86e+01 angle pdb=" N ILE A 250 " pdb=" CA ILE A 250 " pdb=" C ILE A 250 " ideal model delta sigma weight residual 106.21 113.52 -7.31 1.07e+00 8.73e-01 4.67e+01 angle pdb=" CA ILE A 250 " pdb=" C ILE A 250 " pdb=" O ILE A 250 " ideal model delta sigma weight residual 122.63 118.63 4.00 8.70e-01 1.32e+00 2.12e+01 angle pdb=" C TYR A 249 " pdb=" N ILE A 250 " pdb=" CA ILE A 250 " ideal model delta sigma weight residual 121.65 125.47 -3.82 9.40e-01 1.13e+00 1.65e+01 ... (remaining 10878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 4239 17.80 - 35.60: 484 35.60 - 53.40: 137 53.40 - 71.20: 20 71.20 - 89.00: 11 Dihedral angle restraints: 4891 sinusoidal: 1986 harmonic: 2905 Sorted by residual: dihedral pdb=" CB CYS A 728 " pdb=" SG CYS A 728 " pdb=" SG CYS A 805 " pdb=" CB CYS A 805 " ideal model delta sinusoidal sigma weight residual 93.00 51.73 41.27 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" CA ALA A 851 " pdb=" C ALA A 851 " pdb=" N THR A 852 " pdb=" CA THR A 852 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASN A 596 " pdb=" C ASN A 596 " pdb=" N LEU A 597 " pdb=" CA LEU A 597 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1065 0.074 - 0.148: 119 0.148 - 0.222: 3 0.222 - 0.296: 3 0.296 - 0.370: 3 Chirality restraints: 1193 Sorted by residual: chirality pdb=" CA SER A 253 " pdb=" N SER A 253 " pdb=" C SER A 253 " pdb=" CB SER A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA LEU A 251 " pdb=" N LEU A 251 " pdb=" C LEU A 251 " pdb=" CB LEU A 251 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA MET A 357 " pdb=" N MET A 357 " pdb=" C MET A 357 " pdb=" CB MET A 357 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1190 not shown) Planarity restraints: 1405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 249 " -0.014 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C TYR A 249 " 0.052 2.00e-02 2.50e+03 pdb=" O TYR A 249 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE A 250 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 356 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C ASN A 356 " 0.041 2.00e-02 2.50e+03 pdb=" O ASN A 356 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 357 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 973 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO A 974 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 974 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 974 " -0.028 5.00e-02 4.00e+02 ... (remaining 1402 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 115 2.57 - 3.15: 6711 3.15 - 3.73: 12535 3.73 - 4.32: 16181 4.32 - 4.90: 26669 Nonbonded interactions: 62211 Sorted by model distance: nonbonded pdb=" O TRP A 219 " pdb=" CG2 VAL A 220 " model vdw 1.982 3.460 nonbonded pdb=" O ARG A1085 " pdb=" NZ LYS A1089 " model vdw 2.218 3.120 nonbonded pdb=" NH2 ARG A 519 " pdb=" O ILE A 565 " model vdw 2.221 3.120 nonbonded pdb=" OD2 ASP A 590 " pdb=" OG1 THR A 592 " model vdw 2.234 3.040 nonbonded pdb=" OG SER A 754 " pdb=" OE2 GLU A 755 " model vdw 2.247 3.040 ... (remaining 62206 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.540 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8052 Z= 0.266 Angle : 0.737 10.419 10883 Z= 0.456 Chirality : 0.049 0.370 1193 Planarity : 0.004 0.050 1405 Dihedral : 16.684 89.002 3014 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.92 % Favored : 86.98 % Rotamer: Outliers : 7.85 % Allowed : 20.52 % Favored : 71.63 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.44 % 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: -3.60 (0.24), residues: 991 helix: -0.59 (0.25), residues: 347 sheet: -3.80 (0.38), residues: 101 loop : -3.49 (0.23), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1092 HIS 0.002 0.001 HIS A 445 PHE 0.011 0.001 PHE A 576 TYR 0.013 0.001 TYR A 998 ARG 0.003 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 261 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7120 (mm-30) REVERT: A 337 LEU cc_start: 0.8595 (tp) cc_final: 0.8313 (tp) REVERT: A 376 ARG cc_start: 0.8054 (mtp-110) cc_final: 0.7721 (ttm110) REVERT: A 416 GLU cc_start: 0.8373 (tp30) cc_final: 0.8049 (tp30) REVERT: A 489 GLU cc_start: 0.7408 (tp30) cc_final: 0.7029 (tp30) REVERT: A 513 GLN cc_start: 0.8251 (tt0) cc_final: 0.7978 (tt0) REVERT: A 663 GLU cc_start: 0.8266 (pp20) cc_final: 0.7785 (pp20) REVERT: A 696 LEU cc_start: 0.8154 (tp) cc_final: 0.7848 (tp) REVERT: A 781 LEU cc_start: 0.8054 (mt) cc_final: 0.7602 (mt) REVERT: A 828 ASP cc_start: 0.8332 (t70) cc_final: 0.8018 (t70) REVERT: A 867 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7789 (mm-40) REVERT: A 874 MET cc_start: 0.7354 (ttm) cc_final: 0.7085 (ttm) REVERT: A 889 HIS cc_start: 0.7486 (m170) cc_final: 0.7187 (m-70) REVERT: A 914 ASP cc_start: 0.7708 (t70) cc_final: 0.7319 (t0) REVERT: A 981 ASP cc_start: 0.8030 (t0) cc_final: 0.7797 (t0) REVERT: A 983 GLU cc_start: 0.8545 (pp20) cc_final: 0.8189 (pp20) REVERT: A 995 GLU cc_start: 0.8379 (tp30) cc_final: 0.7493 (tp30) REVERT: A 999 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8007 (mm-30) outliers start: 67 outliers final: 45 residues processed: 306 average time/residue: 0.2475 time to fit residues: 96.5760 Evaluate side-chains 274 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 228 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 867 GLN Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 976 CYS Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1115 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS A 285 ASN A 346 GLN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN A 471 GLN A 596 ASN A 617 ASN A 739 GLN A 747 ASN A 909 HIS A1078 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8052 Z= 0.235 Angle : 0.698 11.936 10883 Z= 0.354 Chirality : 0.046 0.189 1193 Planarity : 0.005 0.053 1405 Dihedral : 8.840 59.626 1181 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 6.80 % Allowed : 25.21 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.26), residues: 991 helix: 0.49 (0.27), residues: 356 sheet: -3.34 (0.39), residues: 107 loop : -3.11 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1076 HIS 0.006 0.001 HIS A 497 PHE 0.021 0.002 PHE A 435 TYR 0.021 0.002 TYR A 291 ARG 0.009 0.001 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 246 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8107 (m-80) cc_final: 0.7797 (m-10) REVERT: A 233 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7228 (mm-30) REVERT: A 251 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7440 (mp) REVERT: A 337 LEU cc_start: 0.8617 (tp) cc_final: 0.8336 (tp) REVERT: A 376 ARG cc_start: 0.8215 (mtp-110) cc_final: 0.7839 (ttm110) REVERT: A 402 SER cc_start: 0.9014 (t) cc_final: 0.8643 (m) REVERT: A 416 GLU cc_start: 0.8318 (tp30) cc_final: 0.8022 (tp30) REVERT: A 489 GLU cc_start: 0.7407 (tp30) cc_final: 0.6992 (tp30) REVERT: A 513 GLN cc_start: 0.8090 (tt0) cc_final: 0.7765 (tt0) REVERT: A 514 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8818 (tt) REVERT: A 595 PHE cc_start: 0.5452 (OUTLIER) cc_final: 0.4854 (t80) REVERT: A 606 PHE cc_start: 0.6593 (p90) cc_final: 0.6245 (p90) REVERT: A 707 ARG cc_start: 0.7787 (mmm-85) cc_final: 0.7574 (mmm-85) REVERT: A 736 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: A 781 LEU cc_start: 0.8243 (mt) cc_final: 0.7812 (mt) REVERT: A 828 ASP cc_start: 0.8271 (t70) cc_final: 0.8045 (t70) REVERT: A 842 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8552 (ttpp) REVERT: A 867 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7771 (mm-40) REVERT: A 873 TYR cc_start: 0.8988 (t80) cc_final: 0.8758 (t80) REVERT: A 896 LYS cc_start: 0.7571 (mtmt) cc_final: 0.7317 (mtmt) REVERT: A 914 ASP cc_start: 0.7753 (t70) cc_final: 0.7354 (t0) REVERT: A 981 ASP cc_start: 0.7882 (t0) cc_final: 0.7609 (t0) REVERT: A 983 GLU cc_start: 0.8537 (pp20) cc_final: 0.8120 (pp20) REVERT: A 995 GLU cc_start: 0.8401 (tp30) cc_final: 0.7400 (tp30) REVERT: A 999 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8046 (mm-30) outliers start: 58 outliers final: 41 residues processed: 287 average time/residue: 0.2138 time to fit residues: 81.4519 Evaluate side-chains 272 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 225 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 867 GLN Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 0.0370 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 72 optimal weight: 0.0670 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 310 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 596 ASN A 614 ASN A1082 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8052 Z= 0.180 Angle : 0.684 14.182 10883 Z= 0.339 Chirality : 0.045 0.217 1193 Planarity : 0.004 0.054 1405 Dihedral : 7.829 59.053 1149 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 5.51 % Allowed : 28.14 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.26), residues: 991 helix: 0.94 (0.27), residues: 356 sheet: -3.00 (0.38), residues: 130 loop : -2.91 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1076 HIS 0.003 0.001 HIS A 816 PHE 0.020 0.002 PHE A 870 TYR 0.018 0.001 TYR A 291 ARG 0.005 0.000 ARG A 853 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 246 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8046 (m-80) cc_final: 0.7796 (m-10) REVERT: A 233 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7154 (mm-30) REVERT: A 309 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.6901 (ptm160) REVERT: A 337 LEU cc_start: 0.8600 (tp) cc_final: 0.8321 (tp) REVERT: A 376 ARG cc_start: 0.8144 (mtp-110) cc_final: 0.7775 (ttm110) REVERT: A 387 LEU cc_start: 0.8727 (mt) cc_final: 0.8450 (mp) REVERT: A 402 SER cc_start: 0.8998 (t) cc_final: 0.8656 (m) REVERT: A 416 GLU cc_start: 0.8278 (tp30) cc_final: 0.8034 (tp30) REVERT: A 467 PHE cc_start: 0.8350 (p90) cc_final: 0.8015 (p90) REVERT: A 475 ASN cc_start: 0.8227 (m-40) cc_final: 0.7938 (m-40) REVERT: A 489 GLU cc_start: 0.7483 (tp30) cc_final: 0.7060 (tp30) REVERT: A 497 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.7837 (t-90) REVERT: A 700 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7920 (mp) REVERT: A 716 LYS cc_start: 0.8637 (ttmm) cc_final: 0.7945 (ttpp) REVERT: A 736 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8374 (tm-30) REVERT: A 802 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8437 (tt) REVERT: A 873 TYR cc_start: 0.8869 (t80) cc_final: 0.8133 (t80) REVERT: A 874 MET cc_start: 0.7160 (ttm) cc_final: 0.6943 (ttm) REVERT: A 896 LYS cc_start: 0.7625 (mtmt) cc_final: 0.7280 (mtmt) REVERT: A 914 ASP cc_start: 0.7495 (t70) cc_final: 0.7172 (t0) REVERT: A 923 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: A 983 GLU cc_start: 0.8476 (pp20) cc_final: 0.8012 (pp20) REVERT: A 995 GLU cc_start: 0.8416 (tp30) cc_final: 0.7326 (tp30) REVERT: A 999 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8067 (mm-30) REVERT: A 1003 GLU cc_start: 0.7910 (pp20) cc_final: 0.7493 (pp20) REVERT: A 1094 PHE cc_start: 0.8033 (t80) cc_final: 0.7771 (t80) outliers start: 47 outliers final: 29 residues processed: 279 average time/residue: 0.2131 time to fit residues: 78.4523 Evaluate side-chains 266 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 923 GLU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 520 GLN A 596 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.004 0.042 8052 Z= 0.258 Angle : 0.700 12.027 10883 Z= 0.355 Chirality : 0.046 0.190 1193 Planarity : 0.005 0.053 1405 Dihedral : 7.389 57.953 1128 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 7.27 % Allowed : 28.25 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.26), residues: 991 helix: 0.99 (0.27), residues: 360 sheet: -2.88 (0.39), residues: 130 loop : -2.80 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1076 HIS 0.006 0.001 HIS A 497 PHE 0.017 0.002 PHE A 870 TYR 0.020 0.002 TYR A 444 ARG 0.004 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 235 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8126 (m-80) cc_final: 0.7862 (m-10) REVERT: A 233 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7137 (mm-30) REVERT: A 337 LEU cc_start: 0.8615 (tp) cc_final: 0.8329 (tp) REVERT: A 376 ARG cc_start: 0.8197 (mtp-110) cc_final: 0.7846 (ttm110) REVERT: A 387 LEU cc_start: 0.8771 (mt) cc_final: 0.8485 (mp) REVERT: A 402 SER cc_start: 0.8994 (t) cc_final: 0.8644 (m) REVERT: A 416 GLU cc_start: 0.8288 (tp30) cc_final: 0.8071 (tp30) REVERT: A 475 ASN cc_start: 0.8276 (m-40) cc_final: 0.7841 (m-40) REVERT: A 489 GLU cc_start: 0.7542 (tp30) cc_final: 0.7109 (tp30) REVERT: A 514 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8872 (tt) REVERT: A 534 ASP cc_start: 0.7434 (p0) cc_final: 0.7217 (p0) REVERT: A 577 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7233 (tm-30) REVERT: A 595 PHE cc_start: 0.5652 (OUTLIER) cc_final: 0.5084 (t80) REVERT: A 620 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7317 (pmmt) REVERT: A 654 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7281 (tm-30) REVERT: A 658 MET cc_start: 0.7413 (ptm) cc_final: 0.7150 (ptm) REVERT: A 696 LEU cc_start: 0.8296 (tp) cc_final: 0.8083 (tp) REVERT: A 707 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7592 (mmm-85) REVERT: A 716 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8472 (ttpp) REVERT: A 736 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8388 (tm-30) REVERT: A 781 LEU cc_start: 0.8238 (mt) cc_final: 0.7821 (mt) REVERT: A 798 ASP cc_start: 0.8319 (t0) cc_final: 0.8079 (m-30) REVERT: A 842 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8438 (ttpp) REVERT: A 867 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7783 (mm-40) REVERT: A 874 MET cc_start: 0.7277 (ttm) cc_final: 0.6996 (ttm) REVERT: A 914 ASP cc_start: 0.7610 (t70) cc_final: 0.7289 (t0) REVERT: A 923 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: A 981 ASP cc_start: 0.7937 (t0) cc_final: 0.7660 (t0) REVERT: A 983 GLU cc_start: 0.8514 (pp20) cc_final: 0.8162 (pp20) REVERT: A 995 GLU cc_start: 0.8481 (tp30) cc_final: 0.7439 (tp30) REVERT: A 999 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8115 (mm-30) outliers start: 62 outliers final: 42 residues processed: 274 average time/residue: 0.2101 time to fit residues: 76.1418 Evaluate side-chains 281 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 232 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 867 GLN Chi-restraints excluded: chain A residue 923 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 0.0070 chunk 39 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8052 Z= 0.189 Angle : 0.674 12.419 10883 Z= 0.336 Chirality : 0.044 0.169 1193 Planarity : 0.004 0.053 1405 Dihedral : 7.041 59.678 1125 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 6.57 % Allowed : 29.78 % Favored : 63.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.27), residues: 991 helix: 1.10 (0.27), residues: 360 sheet: -2.76 (0.40), residues: 130 loop : -2.64 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A1076 HIS 0.004 0.001 HIS A 497 PHE 0.018 0.002 PHE A 515 TYR 0.021 0.002 TYR A 444 ARG 0.004 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 236 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8092 (m-80) cc_final: 0.7797 (m-10) REVERT: A 233 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7174 (mm-30) REVERT: A 337 LEU cc_start: 0.8614 (tp) cc_final: 0.8323 (tp) REVERT: A 376 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.7818 (ttm110) REVERT: A 387 LEU cc_start: 0.8724 (mt) cc_final: 0.8448 (mp) REVERT: A 402 SER cc_start: 0.8927 (t) cc_final: 0.8602 (m) REVERT: A 467 PHE cc_start: 0.8366 (p90) cc_final: 0.8042 (p90) REVERT: A 489 GLU cc_start: 0.7535 (tp30) cc_final: 0.7090 (tp30) REVERT: A 497 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.8293 (t-170) REVERT: A 514 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8944 (tt) REVERT: A 534 ASP cc_start: 0.7389 (p0) cc_final: 0.7163 (p0) REVERT: A 577 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7160 (tm-30) REVERT: A 595 PHE cc_start: 0.5276 (OUTLIER) cc_final: 0.4528 (t80) REVERT: A 606 PHE cc_start: 0.6507 (p90) cc_final: 0.6229 (p90) REVERT: A 614 ASN cc_start: 0.8688 (m110) cc_final: 0.8173 (m-40) REVERT: A 654 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7239 (tm-30) REVERT: A 658 MET cc_start: 0.7265 (ptm) cc_final: 0.7027 (ptm) REVERT: A 683 MET cc_start: 0.8587 (ptp) cc_final: 0.8367 (ptm) REVERT: A 716 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8413 (ttpp) REVERT: A 736 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: A 798 ASP cc_start: 0.8246 (t0) cc_final: 0.8043 (m-30) REVERT: A 842 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8406 (ttpp) REVERT: A 874 MET cc_start: 0.7268 (ttm) cc_final: 0.7047 (ttm) REVERT: A 914 ASP cc_start: 0.7476 (t70) cc_final: 0.7177 (t0) REVERT: A 923 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: A 983 GLU cc_start: 0.8427 (pp20) cc_final: 0.7962 (pp20) REVERT: A 995 GLU cc_start: 0.8431 (tp30) cc_final: 0.7574 (tp30) REVERT: A 999 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8104 (mm-30) REVERT: A 1003 GLU cc_start: 0.7911 (pp20) cc_final: 0.7664 (pp20) REVERT: A 1044 ASP cc_start: 0.8472 (t0) cc_final: 0.8221 (t0) REVERT: A 1096 TRP cc_start: 0.8188 (m100) cc_final: 0.7851 (m100) outliers start: 56 outliers final: 39 residues processed: 272 average time/residue: 0.2045 time to fit residues: 73.9583 Evaluate side-chains 273 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 923 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8052 Z= 0.246 Angle : 0.710 16.274 10883 Z= 0.351 Chirality : 0.046 0.183 1193 Planarity : 0.005 0.053 1405 Dihedral : 7.141 56.454 1125 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 7.50 % Allowed : 30.36 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.27), residues: 991 helix: 1.01 (0.27), residues: 362 sheet: -2.70 (0.41), residues: 130 loop : -2.65 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A1076 HIS 0.003 0.001 HIS A 859 PHE 0.019 0.002 PHE A 515 TYR 0.028 0.002 TYR A 873 ARG 0.004 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 230 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8143 (m-80) cc_final: 0.7798 (m-10) REVERT: A 226 THR cc_start: 0.9050 (m) cc_final: 0.8759 (t) REVERT: A 233 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7191 (mm-30) REVERT: A 337 LEU cc_start: 0.8603 (tp) cc_final: 0.8306 (tp) REVERT: A 376 ARG cc_start: 0.8196 (mtp-110) cc_final: 0.7862 (ttm110) REVERT: A 387 LEU cc_start: 0.8743 (mt) cc_final: 0.8463 (mp) REVERT: A 402 SER cc_start: 0.8953 (t) cc_final: 0.8611 (m) REVERT: A 489 GLU cc_start: 0.7534 (tp30) cc_final: 0.7104 (tp30) REVERT: A 497 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.8239 (t-170) REVERT: A 534 ASP cc_start: 0.7443 (p0) cc_final: 0.7117 (p0) REVERT: A 577 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7124 (tm-30) REVERT: A 595 PHE cc_start: 0.5412 (OUTLIER) cc_final: 0.4575 (t80) REVERT: A 614 ASN cc_start: 0.8718 (m110) cc_final: 0.8289 (m-40) REVERT: A 654 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 658 MET cc_start: 0.7403 (ptm) cc_final: 0.7121 (ptm) REVERT: A 671 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7988 (ptpp) REVERT: A 683 MET cc_start: 0.8542 (ptp) cc_final: 0.8334 (ptt) REVERT: A 707 ARG cc_start: 0.7818 (mmm-85) cc_final: 0.7607 (mmm-85) REVERT: A 716 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8471 (ttpp) REVERT: A 736 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: A 798 ASP cc_start: 0.8310 (t0) cc_final: 0.8101 (m-30) REVERT: A 842 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8394 (ttpp) REVERT: A 867 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7747 (mm-40) REVERT: A 874 MET cc_start: 0.7294 (ttm) cc_final: 0.7069 (ttm) REVERT: A 914 ASP cc_start: 0.7464 (t70) cc_final: 0.7203 (t0) REVERT: A 923 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7723 (pm20) REVERT: A 983 GLU cc_start: 0.8455 (pp20) cc_final: 0.8119 (pp20) REVERT: A 1005 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8282 (tt) outliers start: 64 outliers final: 43 residues processed: 272 average time/residue: 0.1975 time to fit residues: 71.8580 Evaluate side-chains 272 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 221 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 867 GLN Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 923 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.0010 chunk 38 optimal weight: 6.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 596 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8052 Z= 0.187 Angle : 0.715 13.411 10883 Z= 0.348 Chirality : 0.045 0.181 1193 Planarity : 0.004 0.053 1405 Dihedral : 6.891 59.400 1125 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 6.21 % Allowed : 32.94 % Favored : 60.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.27), residues: 991 helix: 1.08 (0.27), residues: 362 sheet: -2.58 (0.42), residues: 132 loop : -2.55 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1076 HIS 0.002 0.001 HIS A 869 PHE 0.033 0.002 PHE A 435 TYR 0.030 0.002 TYR A 873 ARG 0.004 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 232 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8153 (m-80) cc_final: 0.7751 (m-10) REVERT: A 226 THR cc_start: 0.9038 (m) cc_final: 0.8759 (t) REVERT: A 233 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 337 LEU cc_start: 0.8638 (tp) cc_final: 0.8366 (tp) REVERT: A 376 ARG cc_start: 0.8138 (mtp-110) cc_final: 0.7790 (ttm110) REVERT: A 387 LEU cc_start: 0.8684 (mt) cc_final: 0.8433 (mp) REVERT: A 489 GLU cc_start: 0.7527 (tp30) cc_final: 0.7105 (tp30) REVERT: A 497 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.8271 (t-170) REVERT: A 534 ASP cc_start: 0.7312 (p0) cc_final: 0.6984 (p0) REVERT: A 577 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7033 (tm-30) REVERT: A 595 PHE cc_start: 0.5204 (OUTLIER) cc_final: 0.4364 (t80) REVERT: A 614 ASN cc_start: 0.8621 (m110) cc_final: 0.8206 (m-40) REVERT: A 620 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7222 (pmmt) REVERT: A 654 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7265 (tm-30) REVERT: A 658 MET cc_start: 0.7263 (ptm) cc_final: 0.7020 (ptm) REVERT: A 671 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7929 (ptpp) REVERT: A 736 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8379 (tm-30) REVERT: A 798 ASP cc_start: 0.8220 (t0) cc_final: 0.8004 (m-30) REVERT: A 896 LYS cc_start: 0.7724 (mtmt) cc_final: 0.7426 (mtmt) REVERT: A 914 ASP cc_start: 0.7301 (t70) cc_final: 0.7073 (t0) REVERT: A 923 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: A 983 GLU cc_start: 0.8383 (pp20) cc_final: 0.8031 (pp20) outliers start: 53 outliers final: 41 residues processed: 265 average time/residue: 0.2053 time to fit residues: 72.2709 Evaluate side-chains 264 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 217 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 805 CYS Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 923 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8052 Z= 0.244 Angle : 0.762 14.533 10883 Z= 0.374 Chirality : 0.047 0.213 1193 Planarity : 0.005 0.053 1405 Dihedral : 6.915 58.334 1123 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 6.68 % Allowed : 33.18 % Favored : 60.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.27), residues: 991 helix: 1.04 (0.27), residues: 360 sheet: -2.60 (0.42), residues: 122 loop : -2.56 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A1076 HIS 0.003 0.001 HIS A 859 PHE 0.036 0.002 PHE A 435 TYR 0.031 0.002 TYR A 873 ARG 0.004 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 225 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8221 (m-80) cc_final: 0.7742 (m-10) REVERT: A 226 THR cc_start: 0.9052 (m) cc_final: 0.8739 (t) REVERT: A 233 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7201 (mm-30) REVERT: A 337 LEU cc_start: 0.8630 (tp) cc_final: 0.8344 (tp) REVERT: A 376 ARG cc_start: 0.8161 (mtp-110) cc_final: 0.7800 (ttm110) REVERT: A 387 LEU cc_start: 0.8750 (mt) cc_final: 0.8492 (mp) REVERT: A 489 GLU cc_start: 0.7544 (tp30) cc_final: 0.7102 (tp30) REVERT: A 497 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.8325 (t-170) REVERT: A 577 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7036 (tm-30) REVERT: A 595 PHE cc_start: 0.5402 (OUTLIER) cc_final: 0.4494 (t80) REVERT: A 614 ASN cc_start: 0.8667 (m110) cc_final: 0.8240 (m-40) REVERT: A 620 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7243 (pmmt) REVERT: A 654 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7307 (tm-30) REVERT: A 658 MET cc_start: 0.7403 (ptm) cc_final: 0.7145 (ptm) REVERT: A 671 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7978 (ptpp) REVERT: A 707 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7609 (mmm-85) REVERT: A 736 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8390 (tm-30) REVERT: A 896 LYS cc_start: 0.7670 (mtmt) cc_final: 0.7341 (mtmt) REVERT: A 923 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: A 983 GLU cc_start: 0.8429 (pp20) cc_final: 0.8120 (pp20) REVERT: A 1003 GLU cc_start: 0.7765 (pp20) cc_final: 0.7336 (pp20) REVERT: A 1094 PHE cc_start: 0.8089 (t80) cc_final: 0.7808 (t80) outliers start: 57 outliers final: 43 residues processed: 261 average time/residue: 0.2040 time to fit residues: 70.7405 Evaluate side-chains 260 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 211 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 923 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 596 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8052 Z= 0.232 Angle : 0.774 14.396 10883 Z= 0.383 Chirality : 0.047 0.230 1193 Planarity : 0.005 0.053 1405 Dihedral : 6.896 59.091 1123 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 6.10 % Allowed : 34.35 % Favored : 59.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.26), residues: 991 helix: 0.96 (0.27), residues: 361 sheet: -2.63 (0.41), residues: 123 loop : -2.53 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1076 HIS 0.003 0.001 HIS A 859 PHE 0.033 0.002 PHE A 435 TYR 0.018 0.002 TYR A 291 ARG 0.004 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 217 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8252 (m-80) cc_final: 0.7760 (m-10) REVERT: A 226 THR cc_start: 0.9025 (m) cc_final: 0.8729 (t) REVERT: A 233 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7186 (mm-30) REVERT: A 337 LEU cc_start: 0.8613 (tp) cc_final: 0.8334 (tp) REVERT: A 376 ARG cc_start: 0.8165 (mtp-110) cc_final: 0.7793 (ttm110) REVERT: A 387 LEU cc_start: 0.8723 (mt) cc_final: 0.8476 (mp) REVERT: A 489 GLU cc_start: 0.7550 (tp30) cc_final: 0.7108 (tp30) REVERT: A 497 HIS cc_start: 0.8529 (OUTLIER) cc_final: 0.8303 (t-170) REVERT: A 577 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7042 (tm-30) REVERT: A 595 PHE cc_start: 0.5396 (OUTLIER) cc_final: 0.4459 (t80) REVERT: A 614 ASN cc_start: 0.8657 (m110) cc_final: 0.8234 (m-40) REVERT: A 620 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7222 (pmmt) REVERT: A 654 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7301 (tm-30) REVERT: A 658 MET cc_start: 0.7364 (ptm) cc_final: 0.7109 (ptm) REVERT: A 671 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7993 (ptpp) REVERT: A 736 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8396 (tm-30) REVERT: A 896 LYS cc_start: 0.7672 (mtmt) cc_final: 0.7351 (mtmt) REVERT: A 923 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: A 983 GLU cc_start: 0.8407 (pp20) cc_final: 0.8105 (pp20) REVERT: A 1003 GLU cc_start: 0.7743 (pp20) cc_final: 0.7300 (pp20) outliers start: 52 outliers final: 41 residues processed: 246 average time/residue: 0.2018 time to fit residues: 66.0182 Evaluate side-chains 261 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 214 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 923 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 0.0980 chunk 90 optimal weight: 0.0970 chunk 78 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 83 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8052 Z= 0.212 Angle : 0.782 14.094 10883 Z= 0.385 Chirality : 0.047 0.247 1193 Planarity : 0.005 0.053 1405 Dihedral : 6.826 59.476 1122 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 5.51 % Allowed : 35.40 % Favored : 59.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.26), residues: 991 helix: 0.94 (0.27), residues: 357 sheet: -2.50 (0.42), residues: 121 loop : -2.48 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP A1076 HIS 0.003 0.001 HIS A1054 PHE 0.065 0.002 PHE A1094 TYR 0.022 0.002 TYR A 444 ARG 0.005 0.000 ARG A 429 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 222 time to evaluate : 0.942 Fit side-chains REVERT: A 186 TYR cc_start: 0.8228 (m-80) cc_final: 0.7811 (m-10) REVERT: A 226 THR cc_start: 0.8992 (m) cc_final: 0.8722 (t) REVERT: A 233 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7182 (mm-30) REVERT: A 337 LEU cc_start: 0.8642 (tp) cc_final: 0.8383 (tp) REVERT: A 387 LEU cc_start: 0.8692 (mt) cc_final: 0.8440 (mp) REVERT: A 470 SER cc_start: 0.8913 (m) cc_final: 0.8600 (p) REVERT: A 471 GLN cc_start: 0.8260 (mt0) cc_final: 0.8006 (mt0) REVERT: A 489 GLU cc_start: 0.7544 (tp30) cc_final: 0.7124 (tp30) REVERT: A 511 MET cc_start: 0.7801 (ptp) cc_final: 0.7253 (mtm) REVERT: A 577 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7052 (tm-30) REVERT: A 595 PHE cc_start: 0.5155 (OUTLIER) cc_final: 0.4306 (t80) REVERT: A 614 ASN cc_start: 0.8593 (m110) cc_final: 0.8183 (m-40) REVERT: A 620 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7153 (pmmt) REVERT: A 654 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 658 MET cc_start: 0.7321 (ptm) cc_final: 0.7074 (ptm) REVERT: A 671 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7948 (ptpp) REVERT: A 736 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8402 (tm-30) REVERT: A 793 TYR cc_start: 0.7486 (t80) cc_final: 0.7138 (t80) REVERT: A 896 LYS cc_start: 0.7737 (mtmt) cc_final: 0.7418 (mtmt) REVERT: A 923 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: A 983 GLU cc_start: 0.8344 (pp20) cc_final: 0.8077 (pp20) REVERT: A 995 GLU cc_start: 0.7965 (tp30) cc_final: 0.7733 (tp30) REVERT: A 1003 GLU cc_start: 0.7736 (pp20) cc_final: 0.7284 (pp20) REVERT: A 1044 ASP cc_start: 0.8466 (t0) cc_final: 0.8216 (t0) REVERT: A 1092 TRP cc_start: 0.7687 (m100) cc_final: 0.7361 (m100) outliers start: 47 outliers final: 38 residues processed: 249 average time/residue: 0.2061 time to fit residues: 68.3124 Evaluate side-chains 259 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 216 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 923 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 32 optimal weight: 0.1980 chunk 80 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS A 276 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 889 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.104622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094160 restraints weight = 18558.126| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.49 r_work: 0.3287 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8052 Z= 0.314 Angle : 0.823 14.931 10883 Z= 0.412 Chirality : 0.049 0.355 1193 Planarity : 0.005 0.053 1405 Dihedral : 7.071 58.943 1121 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 5.86 % Allowed : 34.58 % Favored : 59.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.26), residues: 991 helix: 0.79 (0.27), residues: 356 sheet: -2.76 (0.42), residues: 119 loop : -2.54 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP A1076 HIS 0.004 0.001 HIS A 859 PHE 0.056 0.003 PHE A1094 TYR 0.042 0.003 TYR A 873 ARG 0.005 0.001 ARG A 429 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.08 seconds wall clock time: 40 minutes 33.03 seconds (2433.03 seconds total)