Starting phenix.real_space_refine on Thu Jun 12 11:21:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w84_32351/06_2025/7w84_32351.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w84_32351/06_2025/7w84_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/cci-nas-00/data/ceres_data/7w84_32351/06_2025/7w84_32351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w84_32351/06_2025/7w84_32351.map" model { file = "/net/cci-nas-00/data/ceres_data/7w84_32351/06_2025/7w84_32351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w84_32351/06_2025/7w84_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-5710/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: 5.18, per 1000 atoms: 0.66 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: 2.15 Conformation dependent library (CDL) restraints added in 874.9 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: 0.87 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: 2.48 Time building geometry restraints manager: 2.31 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: 1.250 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.130 Find NCS groups from input model: 0.070 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.600 ------------------------------------------------------------------------------- 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 8053 Z= 0.224 Angle : 0.737 10.419 10885 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 Details of bonding type rmsd hydrogen bonds : bond 0.12715 ( 309) hydrogen bonds : angle 6.22740 ( 855) SS BOND : bond 0.00801 ( 1) SS BOND : angle 0.37686 ( 2) covalent geometry : bond 0.00400 ( 8052) covalent geometry : angle 0.73749 (10883) *********************** 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 to be fit. rotamer outliers: 67 poor density : 261 time to evaluate : 0.856 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: 0.2411 time to fit residues: 94.3890 Evaluate side-chains 274 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.103880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.093762 restraints weight = 18674.436| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.44 r_work: 0.3273 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 8053 Z= 0.160 Angle : 0.698 11.936 10885 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 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 309) hydrogen bonds : angle 5.17440 ( 855) SS BOND : bond 0.00374 ( 1) SS BOND : angle 0.28995 ( 2) covalent geometry : bond 0.00361 ( 8052) covalent geometry : angle 0.69768 (10883) *********************** 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 to be fit. rotamer outliers: 58 poor density : 246 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8384 (m-80) cc_final: 0.8028 (m-10) REVERT: A 233 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7732 (mm-30) REVERT: A 251 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7520 (mp) REVERT: A 337 LEU cc_start: 0.8648 (tp) cc_final: 0.8367 (tp) REVERT: A 376 ARG cc_start: 0.8576 (mtp-110) cc_final: 0.8207 (ttm110) REVERT: A 402 SER cc_start: 0.9094 (t) cc_final: 0.8755 (m) REVERT: A 416 GLU cc_start: 0.8547 (tp30) cc_final: 0.8248 (tp30) REVERT: A 489 GLU cc_start: 0.7886 (tp30) cc_final: 0.7473 (tp30) REVERT: A 513 GLN cc_start: 0.8388 (tt0) cc_final: 0.8067 (tt0) REVERT: A 514 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8814 (tt) REVERT: A 595 PHE cc_start: 0.5726 (OUTLIER) cc_final: 0.5048 (t80) REVERT: A 606 PHE cc_start: 0.6698 (p90) cc_final: 0.6356 (p90) REVERT: A 736 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8455 (tm-30) REVERT: A 781 LEU cc_start: 0.8351 (mt) cc_final: 0.7920 (mt) REVERT: A 828 ASP cc_start: 0.8387 (t70) cc_final: 0.8150 (t70) REVERT: A 842 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8429 (ttpp) REVERT: A 867 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7948 (mm-40) REVERT: A 873 TYR cc_start: 0.9095 (t80) cc_final: 0.8871 (t80) REVERT: A 896 LYS cc_start: 0.7711 (mtmt) cc_final: 0.7474 (mtmt) REVERT: A 914 ASP cc_start: 0.8161 (t70) cc_final: 0.7720 (t0) REVERT: A 981 ASP cc_start: 0.8153 (t0) cc_final: 0.7835 (t0) REVERT: A 983 GLU cc_start: 0.8709 (pp20) cc_final: 0.8247 (pp20) REVERT: A 995 GLU cc_start: 0.8639 (tp30) cc_final: 0.7767 (tp30) REVERT: A 999 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8379 (mm-30) outliers start: 58 outliers final: 41 residues processed: 287 average time/residue: 0.2063 time to fit residues: 78.6180 Evaluate side-chains 272 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 225 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 88 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 98 optimal weight: 0.0170 chunk 97 optimal weight: 0.2980 chunk 48 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.6222 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.106670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096259 restraints weight = 18815.688| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.52 r_work: 0.3317 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8053 Z= 0.125 Angle : 0.686 14.429 10885 Z= 0.340 Chirality : 0.045 0.217 1193 Planarity : 0.004 0.054 1405 Dihedral : 7.840 59.074 1149 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 5.63 % Allowed : 27.90 % Favored : 66.47 % 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: -2.16 (0.26), residues: 991 helix: 0.94 (0.27), residues: 356 sheet: -2.97 (0.38), residues: 130 loop : -2.90 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1076 HIS 0.004 0.001 HIS A 816 PHE 0.021 0.002 PHE A 870 TYR 0.016 0.001 TYR A 291 ARG 0.006 0.000 ARG A 853 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 309) hydrogen bonds : angle 4.85026 ( 855) SS BOND : bond 0.00560 ( 1) SS BOND : angle 1.18675 ( 2) covalent geometry : bond 0.00278 ( 8052) covalent geometry : angle 0.68592 (10883) *********************** 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 294 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8334 (m-80) cc_final: 0.8043 (m-10) REVERT: A 233 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7666 (mm-30) REVERT: A 309 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.6883 (ptm160) REVERT: A 337 LEU cc_start: 0.8623 (tp) cc_final: 0.8345 (tp) REVERT: A 376 ARG cc_start: 0.8464 (mtp-110) cc_final: 0.8098 (ttm110) REVERT: A 387 LEU cc_start: 0.8857 (mt) cc_final: 0.8577 (mp) REVERT: A 402 SER cc_start: 0.9083 (t) cc_final: 0.8772 (m) REVERT: A 416 GLU cc_start: 0.8530 (tp30) cc_final: 0.8264 (tp30) REVERT: A 467 PHE cc_start: 0.8459 (p90) cc_final: 0.8140 (p90) REVERT: A 475 ASN cc_start: 0.8434 (m-40) cc_final: 0.8214 (m-40) REVERT: A 489 GLU cc_start: 0.7986 (tp30) cc_final: 0.7548 (tp30) REVERT: A 497 HIS cc_start: 0.8729 (OUTLIER) cc_final: 0.8203 (t-90) REVERT: A 652 MET cc_start: 0.8131 (mmm) cc_final: 0.7560 (mmp) REVERT: A 716 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8056 (ttpp) REVERT: A 736 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8431 (tm-30) REVERT: A 802 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8468 (tt) REVERT: A 828 ASP cc_start: 0.8363 (t70) cc_final: 0.8125 (t0) REVERT: A 873 TYR cc_start: 0.8983 (t80) cc_final: 0.8185 (t80) REVERT: A 896 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7421 (mtmt) REVERT: A 914 ASP cc_start: 0.7901 (t70) cc_final: 0.7524 (t0) REVERT: A 923 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7633 (pm20) REVERT: A 983 GLU cc_start: 0.8648 (pp20) cc_final: 0.8135 (pp20) REVERT: A 995 GLU cc_start: 0.8658 (tp30) cc_final: 0.7719 (tp30) REVERT: A 999 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8392 (mm-30) REVERT: A 1094 PHE cc_start: 0.8253 (t80) cc_final: 0.8022 (t80) outliers start: 48 outliers final: 30 residues processed: 278 average time/residue: 0.2509 time to fit residues: 92.1140 Evaluate side-chains 270 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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 706 ASN 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 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 29 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 513 GLN A 596 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.105682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.095324 restraints weight = 18578.457| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.47 r_work: 0.3303 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8053 Z= 0.137 Angle : 0.684 12.468 10885 Z= 0.342 Chirality : 0.045 0.194 1193 Planarity : 0.004 0.054 1405 Dihedral : 7.130 59.703 1128 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 7.15 % Allowed : 27.90 % Favored : 64.95 % 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: -1.92 (0.27), residues: 991 helix: 1.10 (0.27), residues: 360 sheet: -2.89 (0.39), residues: 130 loop : -2.74 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A1076 HIS 0.006 0.001 HIS A 497 PHE 0.016 0.002 PHE A 515 TYR 0.020 0.001 TYR A 444 ARG 0.004 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 309) hydrogen bonds : angle 4.83915 ( 855) SS BOND : bond 0.00441 ( 1) SS BOND : angle 1.25182 ( 2) covalent geometry : bond 0.00309 ( 8052) covalent geometry : angle 0.68368 (10883) *********************** 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 299 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 238 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8350 (m-80) cc_final: 0.8087 (m-10) REVERT: A 233 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7620 (mm-30) REVERT: A 309 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7671 (ptm160) REVERT: A 337 LEU cc_start: 0.8645 (tp) cc_final: 0.8355 (tp) REVERT: A 376 ARG cc_start: 0.8476 (mtp-110) cc_final: 0.8118 (ttm110) REVERT: A 387 LEU cc_start: 0.8840 (mt) cc_final: 0.8549 (mp) REVERT: A 402 SER cc_start: 0.9058 (t) cc_final: 0.8757 (m) REVERT: A 416 GLU cc_start: 0.8520 (tp30) cc_final: 0.8289 (tp30) REVERT: A 489 GLU cc_start: 0.8024 (tp30) cc_final: 0.7562 (tp30) REVERT: A 514 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8855 (tt) REVERT: A 577 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7453 (tm-30) REVERT: A 595 PHE cc_start: 0.5736 (OUTLIER) cc_final: 0.4913 (t80) REVERT: A 652 MET cc_start: 0.8068 (mmm) cc_final: 0.7512 (mmp) REVERT: A 654 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7407 (tm-30) REVERT: A 658 MET cc_start: 0.7546 (ptm) cc_final: 0.7271 (ptm) REVERT: A 696 LEU cc_start: 0.8228 (tp) cc_final: 0.8027 (tp) REVERT: A 736 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8434 (tm-30) REVERT: A 793 TYR cc_start: 0.7954 (t80) cc_final: 0.7577 (t80) REVERT: A 798 ASP cc_start: 0.8473 (t0) cc_final: 0.8201 (m-30) REVERT: A 828 ASP cc_start: 0.8425 (t70) cc_final: 0.8145 (t70) REVERT: A 829 LEU cc_start: 0.8518 (mt) cc_final: 0.8260 (mt) REVERT: A 842 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8306 (ttpp) REVERT: A 867 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7950 (mm-40) REVERT: A 896 LYS cc_start: 0.7769 (mtmt) cc_final: 0.7396 (mtmt) REVERT: A 914 ASP cc_start: 0.7899 (t70) cc_final: 0.7542 (t0) REVERT: A 923 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: A 983 GLU cc_start: 0.8626 (pp20) cc_final: 0.8150 (pp20) REVERT: A 995 GLU cc_start: 0.8684 (tp30) cc_final: 0.7733 (tp30) REVERT: A 999 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8414 (mm-30) REVERT: A 1044 ASP cc_start: 0.8700 (t0) cc_final: 0.8450 (t0) outliers start: 61 outliers final: 41 residues processed: 274 average time/residue: 0.2662 time to fit residues: 99.4087 Evaluate side-chains 280 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 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 498 PHE Chi-restraints excluded: chain A residue 514 LEU 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 646 SER Chi-restraints excluded: chain A residue 703 HIS 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 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 1061 LEU Chi-restraints excluded: chain A residue 1079 VAL 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 58 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 86 optimal weight: 0.0980 chunk 94 optimal weight: 5.9990 chunk 23 optimal weight: 0.0570 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN A 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.108085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.097597 restraints weight = 18508.713| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.52 r_work: 0.3342 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8053 Z= 0.118 Angle : 0.666 12.827 10885 Z= 0.330 Chirality : 0.044 0.169 1193 Planarity : 0.004 0.053 1405 Dihedral : 6.937 58.436 1126 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 6.21 % Allowed : 29.19 % Favored : 64.60 % 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: 1.20 (0.27), residues: 359 sheet: -2.80 (0.39), residues: 132 loop : -2.61 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A1076 HIS 0.004 0.001 HIS A 497 PHE 0.021 0.002 PHE A 467 TYR 0.022 0.001 TYR A 444 ARG 0.004 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 309) hydrogen bonds : angle 4.74055 ( 855) SS BOND : bond 0.00217 ( 1) SS BOND : angle 0.98783 ( 2) covalent geometry : bond 0.00265 ( 8052) covalent geometry : angle 0.66626 (10883) *********************** 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 291 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 238 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8314 (m-80) cc_final: 0.8107 (m-10) REVERT: A 189 ARG cc_start: 0.8650 (mtt180) cc_final: 0.8184 (mtt90) REVERT: A 226 THR cc_start: 0.9166 (m) cc_final: 0.8888 (t) REVERT: A 233 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7621 (mm-30) REVERT: A 309 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7179 (ptm160) REVERT: A 337 LEU cc_start: 0.8655 (tp) cc_final: 0.8368 (tp) REVERT: A 376 ARG cc_start: 0.8408 (mtp-110) cc_final: 0.8054 (ttm110) REVERT: A 387 LEU cc_start: 0.8828 (mt) cc_final: 0.8576 (mp) REVERT: A 402 SER cc_start: 0.9004 (t) cc_final: 0.8726 (m) REVERT: A 489 GLU cc_start: 0.7981 (tp30) cc_final: 0.7556 (tp30) REVERT: A 497 HIS cc_start: 0.8796 (OUTLIER) cc_final: 0.8561 (t-170) REVERT: A 577 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7374 (tm-30) REVERT: A 595 PHE cc_start: 0.5367 (OUTLIER) cc_final: 0.4481 (t80) REVERT: A 620 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7248 (pmmt) REVERT: A 648 GLN cc_start: 0.8521 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 652 MET cc_start: 0.8122 (mmm) cc_final: 0.7431 (mmp) REVERT: A 654 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7425 (tm-30) REVERT: A 658 MET cc_start: 0.7384 (ptm) cc_final: 0.7180 (ptm) REVERT: A 671 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8102 (ptpp) REVERT: A 736 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8442 (tm-30) REVERT: A 793 TYR cc_start: 0.7927 (t80) cc_final: 0.7520 (t80) REVERT: A 798 ASP cc_start: 0.8439 (t0) cc_final: 0.8182 (m-30) REVERT: A 828 ASP cc_start: 0.8422 (t70) cc_final: 0.8137 (t70) REVERT: A 829 LEU cc_start: 0.8419 (mt) cc_final: 0.8212 (mt) REVERT: A 896 LYS cc_start: 0.7796 (mtmt) cc_final: 0.7457 (mtmt) REVERT: A 914 ASP cc_start: 0.7750 (t70) cc_final: 0.7433 (t0) REVERT: A 923 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: A 983 GLU cc_start: 0.8548 (pp20) cc_final: 0.8071 (pp20) REVERT: A 1096 TRP cc_start: 0.8207 (m100) cc_final: 0.7853 (m100) outliers start: 53 outliers final: 36 residues processed: 273 average time/residue: 0.3461 time to fit residues: 128.6655 Evaluate side-chains 270 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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 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 497 HIS Chi-restraints excluded: chain A residue 498 PHE 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 620 LYS Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 706 ASN 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 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 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 1115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.104848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.094459 restraints weight = 18578.768| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.49 r_work: 0.3290 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8053 Z= 0.162 Angle : 0.707 15.293 10885 Z= 0.352 Chirality : 0.046 0.199 1193 Planarity : 0.005 0.053 1405 Dihedral : 7.105 57.887 1125 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 7.03 % Allowed : 30.36 % Favored : 62.60 % 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: 1.11 (0.27), residues: 361 sheet: -2.77 (0.40), residues: 130 loop : -2.64 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A1076 HIS 0.004 0.001 HIS A1054 PHE 0.017 0.002 PHE A 515 TYR 0.025 0.002 TYR A 873 ARG 0.004 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 309) hydrogen bonds : angle 4.91454 ( 855) SS BOND : bond 0.00360 ( 1) SS BOND : angle 0.92360 ( 2) covalent geometry : bond 0.00366 ( 8052) covalent geometry : angle 0.70648 (10883) *********************** 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 290 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 230 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8385 (m-80) cc_final: 0.8017 (m-10) REVERT: A 226 THR cc_start: 0.9153 (m) cc_final: 0.8869 (t) REVERT: A 233 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7626 (mm-30) REVERT: A 337 LEU cc_start: 0.8649 (tp) cc_final: 0.8357 (tp) REVERT: A 376 ARG cc_start: 0.8507 (mtp-110) cc_final: 0.8155 (ttm110) REVERT: A 387 LEU cc_start: 0.8867 (mt) cc_final: 0.8610 (mp) REVERT: A 402 SER cc_start: 0.9033 (t) cc_final: 0.8755 (m) REVERT: A 435 PHE cc_start: 0.7456 (p90) cc_final: 0.7228 (p90) REVERT: A 489 GLU cc_start: 0.8010 (tp30) cc_final: 0.7582 (tp30) REVERT: A 497 HIS cc_start: 0.8780 (OUTLIER) cc_final: 0.8536 (t-170) REVERT: A 514 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8937 (tt) REVERT: A 577 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 595 PHE cc_start: 0.5595 (OUTLIER) cc_final: 0.4714 (t80) REVERT: A 614 ASN cc_start: 0.8575 (m110) cc_final: 0.8132 (m-40) REVERT: A 620 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7289 (pmmt) REVERT: A 654 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 658 MET cc_start: 0.7590 (ptm) cc_final: 0.7331 (ptm) REVERT: A 736 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8422 (tm-30) REVERT: A 781 LEU cc_start: 0.8287 (mt) cc_final: 0.7879 (mt) REVERT: A 828 ASP cc_start: 0.8441 (t70) cc_final: 0.8109 (t0) REVERT: A 829 LEU cc_start: 0.8482 (mt) cc_final: 0.8169 (mt) REVERT: A 842 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8229 (ttpp) REVERT: A 914 ASP cc_start: 0.7810 (t70) cc_final: 0.7493 (t0) REVERT: A 923 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: A 983 GLU cc_start: 0.8586 (pp20) cc_final: 0.8192 (pp20) REVERT: A 999 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8540 (mm-30) REVERT: A 1005 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8379 (tt) outliers start: 60 outliers final: 44 residues processed: 267 average time/residue: 0.2094 time to fit residues: 74.9867 Evaluate side-chains 270 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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 477 VAL 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 620 LYS Chi-restraints excluded: chain A residue 646 SER 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 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 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 1005 LEU 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 1115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 513 GLN A 596 ASN A 889 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.102352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.092194 restraints weight = 19057.911| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.48 r_work: 0.3256 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8053 Z= 0.211 Angle : 0.768 14.407 10885 Z= 0.385 Chirality : 0.048 0.205 1193 Planarity : 0.005 0.053 1405 Dihedral : 7.460 59.695 1125 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.91 % Favored : 88.09 % Rotamer: Outliers : 8.09 % Allowed : 30.25 % Favored : 61.66 % 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: -1.99 (0.26), residues: 991 helix: 0.89 (0.27), residues: 359 sheet: -2.86 (0.42), residues: 118 loop : -2.68 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A1076 HIS 0.005 0.001 HIS A 859 PHE 0.030 0.002 PHE A1094 TYR 0.031 0.002 TYR A 873 ARG 0.004 0.001 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 309) hydrogen bonds : angle 5.21856 ( 855) SS BOND : bond 0.00330 ( 1) SS BOND : angle 1.41455 ( 2) covalent geometry : bond 0.00471 ( 8052) covalent geometry : angle 0.76785 (10883) *********************** 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 293 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 224 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8496 (m-80) cc_final: 0.7975 (m-10) REVERT: A 233 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7720 (mm-30) REVERT: A 337 LEU cc_start: 0.8649 (tp) cc_final: 0.8353 (tp) REVERT: A 376 ARG cc_start: 0.8569 (mtp-110) cc_final: 0.8214 (ttm110) REVERT: A 387 LEU cc_start: 0.8916 (mt) cc_final: 0.8658 (mp) REVERT: A 402 SER cc_start: 0.9047 (t) cc_final: 0.8750 (m) REVERT: A 416 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: A 467 PHE cc_start: 0.8558 (p90) cc_final: 0.8295 (p90) REVERT: A 489 GLU cc_start: 0.8011 (tp30) cc_final: 0.7576 (tp30) REVERT: A 497 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.8571 (t-170) REVERT: A 577 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7404 (tm-30) REVERT: A 595 PHE cc_start: 0.5852 (OUTLIER) cc_final: 0.4981 (t80) REVERT: A 614 ASN cc_start: 0.8692 (m110) cc_final: 0.8329 (m-40) REVERT: A 620 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7360 (pmmt) REVERT: A 654 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7457 (tm-30) REVERT: A 658 MET cc_start: 0.7737 (ptm) cc_final: 0.7449 (ptm) REVERT: A 781 LEU cc_start: 0.8409 (mt) cc_final: 0.8064 (mt) REVERT: A 828 ASP cc_start: 0.8438 (t70) cc_final: 0.8153 (t0) REVERT: A 842 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8275 (ttpp) REVERT: A 914 ASP cc_start: 0.7928 (t70) cc_final: 0.7594 (t0) REVERT: A 923 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: A 983 GLU cc_start: 0.8640 (pp20) cc_final: 0.8276 (pp20) REVERT: A 995 GLU cc_start: 0.8675 (tp30) cc_final: 0.7913 (tp30) REVERT: A 999 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8385 (mm-30) REVERT: A 1003 GLU cc_start: 0.8316 (pp20) cc_final: 0.7984 (pp20) REVERT: A 1005 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8417 (tt) outliers start: 69 outliers final: 51 residues processed: 267 average time/residue: 0.1977 time to fit residues: 71.3392 Evaluate side-chains 278 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 220 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 159 LEU 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 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 416 GLU 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 477 VAL 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 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 706 ASN Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 746 LYS 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 802 LEU Chi-restraints excluded: chain A residue 805 CYS 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 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 1024 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1074 SER 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 36 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.105425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.095014 restraints weight = 18887.133| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.54 r_work: 0.3295 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8053 Z= 0.150 Angle : 0.751 13.170 10885 Z= 0.371 Chirality : 0.047 0.196 1193 Planarity : 0.005 0.053 1405 Dihedral : 7.252 57.559 1125 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 7.03 % Allowed : 32.59 % Favored : 60.38 % 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: -1.93 (0.26), residues: 991 helix: 0.87 (0.27), residues: 361 sheet: -2.62 (0.40), residues: 131 loop : -2.65 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP A1076 HIS 0.002 0.001 HIS A 310 PHE 0.019 0.002 PHE A 515 TYR 0.029 0.002 TYR A 873 ARG 0.004 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 309) hydrogen bonds : angle 5.11035 ( 855) SS BOND : bond 0.00277 ( 1) SS BOND : angle 1.37301 ( 2) covalent geometry : bond 0.00337 ( 8052) covalent geometry : angle 0.75120 (10883) *********************** 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 293 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 233 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8485 (m-80) cc_final: 0.8006 (m-10) REVERT: A 226 THR cc_start: 0.9147 (m) cc_final: 0.8915 (t) REVERT: A 233 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 337 LEU cc_start: 0.8665 (tp) cc_final: 0.8373 (tp) REVERT: A 376 ARG cc_start: 0.8513 (mtp-110) cc_final: 0.8135 (ttm110) REVERT: A 387 LEU cc_start: 0.8866 (mt) cc_final: 0.8632 (mp) REVERT: A 416 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: A 444 TYR cc_start: 0.7541 (t80) cc_final: 0.7236 (t80) REVERT: A 467 PHE cc_start: 0.8501 (p90) cc_final: 0.8213 (p90) REVERT: A 489 GLU cc_start: 0.8023 (tp30) cc_final: 0.7590 (tp30) REVERT: A 577 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7324 (tm-30) REVERT: A 595 PHE cc_start: 0.5704 (OUTLIER) cc_final: 0.4684 (t80) REVERT: A 614 ASN cc_start: 0.8604 (m110) cc_final: 0.8234 (m-40) REVERT: A 620 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7326 (pmmt) REVERT: A 654 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7390 (tm-30) REVERT: A 658 MET cc_start: 0.7559 (ptm) cc_final: 0.7298 (ptm) REVERT: A 781 LEU cc_start: 0.8268 (mt) cc_final: 0.7874 (mt) REVERT: A 828 ASP cc_start: 0.8432 (t70) cc_final: 0.8145 (t0) REVERT: A 829 LEU cc_start: 0.8445 (mt) cc_final: 0.8074 (mt) REVERT: A 842 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8246 (ttpp) REVERT: A 914 ASP cc_start: 0.7724 (t70) cc_final: 0.7425 (t0) REVERT: A 923 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: A 983 GLU cc_start: 0.8566 (pp20) cc_final: 0.8234 (pp20) REVERT: A 995 GLU cc_start: 0.8640 (tp30) cc_final: 0.7966 (tp30) REVERT: A 999 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8388 (mm-30) outliers start: 60 outliers final: 45 residues processed: 273 average time/residue: 0.2256 time to fit residues: 83.6071 Evaluate side-chains 276 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 226 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 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 416 GLU 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 477 VAL 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 706 ASN Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 730 ASP 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 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 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 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 43 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 497 HIS A 596 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.106190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.095647 restraints weight = 18902.800| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.56 r_work: 0.3307 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8053 Z= 0.147 Angle : 0.763 13.453 10885 Z= 0.373 Chirality : 0.047 0.218 1193 Planarity : 0.005 0.053 1405 Dihedral : 7.117 58.290 1123 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % 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: -1.86 (0.26), residues: 991 helix: 0.94 (0.27), residues: 360 sheet: -2.49 (0.41), residues: 131 loop : -2.63 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A1076 HIS 0.008 0.001 HIS A 497 PHE 0.020 0.002 PHE A 515 TYR 0.019 0.002 TYR A 873 ARG 0.005 0.000 ARG A 956 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 309) hydrogen bonds : angle 5.09827 ( 855) SS BOND : bond 0.00341 ( 1) SS BOND : angle 1.85377 ( 2) covalent geometry : bond 0.00330 ( 8052) covalent geometry : angle 0.76255 (10883) *********************** 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 284 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 227 time to evaluate : 1.400 Fit side-chains REVERT: A 186 TYR cc_start: 0.8481 (m-80) cc_final: 0.7995 (m-10) REVERT: A 226 THR cc_start: 0.9142 (m) cc_final: 0.8905 (t) REVERT: A 233 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7721 (mm-30) REVERT: A 337 LEU cc_start: 0.8673 (tp) cc_final: 0.8383 (tp) REVERT: A 376 ARG cc_start: 0.8476 (mtp-110) cc_final: 0.8112 (ttm110) REVERT: A 387 LEU cc_start: 0.8840 (mt) cc_final: 0.8598 (mp) REVERT: A 489 GLU cc_start: 0.8047 (tp30) cc_final: 0.7600 (tp30) REVERT: A 511 MET cc_start: 0.7816 (ptp) cc_final: 0.7317 (mtm) REVERT: A 577 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7303 (tm-30) REVERT: A 595 PHE cc_start: 0.5629 (OUTLIER) cc_final: 0.4546 (t80) REVERT: A 614 ASN cc_start: 0.8622 (m110) cc_final: 0.8253 (m-40) REVERT: A 620 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7281 (pmmt) REVERT: A 654 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7400 (tm-30) REVERT: A 658 MET cc_start: 0.7561 (ptm) cc_final: 0.7320 (ptm) REVERT: A 736 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8441 (tm-30) REVERT: A 789 LEU cc_start: 0.8557 (mt) cc_final: 0.8021 (pp) REVERT: A 828 ASP cc_start: 0.8442 (t70) cc_final: 0.8118 (t0) REVERT: A 829 LEU cc_start: 0.8452 (mt) cc_final: 0.8146 (mt) REVERT: A 842 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8256 (ttpp) REVERT: A 923 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: A 983 GLU cc_start: 0.8560 (pp20) cc_final: 0.8225 (pp20) REVERT: A 995 GLU cc_start: 0.8660 (tp30) cc_final: 0.7985 (tp30) REVERT: A 999 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8422 (mm-30) outliers start: 57 outliers final: 46 residues processed: 260 average time/residue: 0.2993 time to fit residues: 104.9221 Evaluate side-chains 272 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 221 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 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 706 ASN 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 746 LYS 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 842 LYS 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 944 MET 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 87 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.105748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.095344 restraints weight = 18774.901| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.52 r_work: 0.3303 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8053 Z= 0.167 Angle : 0.794 14.459 10885 Z= 0.391 Chirality : 0.047 0.269 1193 Planarity : 0.005 0.055 1405 Dihedral : 7.163 57.624 1123 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 6.21 % Allowed : 33.76 % Favored : 60.02 % 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: -1.87 (0.26), residues: 991 helix: 0.92 (0.27), residues: 359 sheet: -2.45 (0.41), residues: 131 loop : -2.64 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A1076 HIS 0.004 0.001 HIS A 173 PHE 0.019 0.002 PHE A 515 TYR 0.021 0.002 TYR A 998 ARG 0.006 0.001 ARG A 800 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 309) hydrogen bonds : angle 5.12727 ( 855) SS BOND : bond 0.00318 ( 1) SS BOND : angle 1.85092 ( 2) covalent geometry : bond 0.00377 ( 8052) covalent geometry : angle 0.79407 (10883) ********************** 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 278 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 225 time to evaluate : 0.867 Fit side-chains REVERT: A 186 TYR cc_start: 0.8513 (m-80) cc_final: 0.8041 (m-10) REVERT: A 226 THR cc_start: 0.9149 (m) cc_final: 0.8900 (t) REVERT: A 233 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7729 (mm-30) REVERT: A 337 LEU cc_start: 0.8673 (tp) cc_final: 0.8386 (tp) REVERT: A 376 ARG cc_start: 0.8515 (mtp-110) cc_final: 0.8138 (ttm110) REVERT: A 387 LEU cc_start: 0.8872 (mt) cc_final: 0.8631 (mp) REVERT: A 489 GLU cc_start: 0.8059 (tp30) cc_final: 0.7607 (tp30) REVERT: A 511 MET cc_start: 0.7872 (ptp) cc_final: 0.7320 (mtm) REVERT: A 577 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 595 PHE cc_start: 0.5717 (OUTLIER) cc_final: 0.4690 (t80) REVERT: A 614 ASN cc_start: 0.8617 (m110) cc_final: 0.8246 (m-40) REVERT: A 620 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7327 (pmmt) REVERT: A 654 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7396 (tm-30) REVERT: A 658 MET cc_start: 0.7657 (ptm) cc_final: 0.7355 (ptm) REVERT: A 696 LEU cc_start: 0.8030 (tp) cc_final: 0.7809 (mp) REVERT: A 736 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8457 (tm-30) REVERT: A 789 LEU cc_start: 0.8560 (mt) cc_final: 0.8032 (pp) REVERT: A 828 ASP cc_start: 0.8442 (t70) cc_final: 0.8116 (t0) REVERT: A 829 LEU cc_start: 0.8465 (mt) cc_final: 0.8097 (mt) REVERT: A 842 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8268 (ttpp) REVERT: A 923 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: A 983 GLU cc_start: 0.8564 (pp20) cc_final: 0.8254 (pp20) REVERT: A 995 GLU cc_start: 0.8589 (tp30) cc_final: 0.8133 (tp30) REVERT: A 999 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8618 (mm-30) outliers start: 53 outliers final: 46 residues processed: 259 average time/residue: 0.2049 time to fit residues: 70.4976 Evaluate side-chains 270 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 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 706 ASN 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 746 LYS 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 842 LYS 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 944 MET 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 26 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 424 ASN A 471 GLN A 596 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.107304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.096902 restraints weight = 18615.359| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.51 r_work: 0.3331 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8053 Z= 0.149 Angle : 0.789 14.777 10885 Z= 0.388 Chirality : 0.047 0.233 1193 Planarity : 0.005 0.053 1405 Dihedral : 7.086 59.155 1123 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 6.21 % Allowed : 34.00 % Favored : 59.79 % 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: -1.80 (0.26), residues: 991 helix: 0.90 (0.27), residues: 359 sheet: -2.36 (0.42), residues: 130 loop : -2.54 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP A1076 HIS 0.004 0.001 HIS A 173 PHE 0.023 0.002 PHE A 595 TYR 0.028 0.002 TYR A 873 ARG 0.006 0.000 ARG A 800 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 309) hydrogen bonds : angle 5.12375 ( 855) SS BOND : bond 0.00303 ( 1) SS BOND : angle 1.67808 ( 2) covalent geometry : bond 0.00334 ( 8052) covalent geometry : angle 0.78839 (10883) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4496.24 seconds wall clock time: 82 minutes 35.11 seconds (4955.11 seconds total)