Starting phenix.real_space_refine on Fri Jul 19 15:32:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd9_17607/07_2024/8pd9_17607.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd9_17607/07_2024/8pd9_17607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd9_17607/07_2024/8pd9_17607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd9_17607/07_2024/8pd9_17607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd9_17607/07_2024/8pd9_17607.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd9_17607/07_2024/8pd9_17607.cif" } resolution = 3.6 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 41 5.16 5 C 5289 2.51 5 N 1346 2.21 5 O 1430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A ARG 573": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 605": "NH1" <-> "NH2" Residue "A ARG 609": "NH1" <-> "NH2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ARG 803": "NH1" <-> "NH2" Residue "A ARG 806": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 812": "NH1" <-> "NH2" Residue "A ARG 856": "NH1" <-> "NH2" Residue "A ARG 865": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 903": "NH1" <-> "NH2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A ARG 940": "NH1" <-> "NH2" Residue "A ARG 976": "NH1" <-> "NH2" Residue "A ARG 1053": "NH1" <-> "NH2" Residue "A ARG 1092": "NH1" <-> "NH2" Residue "A ARG 1097": "NH1" <-> "NH2" Residue "A ARG 1123": "NH1" <-> "NH2" Residue "A ARG 1158": "NH1" <-> "NH2" Residue "A ARG 1162": "NH1" <-> "NH2" Residue "A ARG 1169": "NH1" <-> "NH2" Residue "A ARG 1185": "NH1" <-> "NH2" Residue "A ARG 1190": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8107 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8085 Classifications: {'peptide': 1024} Link IDs: {'PTRANS': 30, 'TRANS': 993} Chain breaks: 5 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 5.22, per 1000 atoms: 0.64 Number of scatterers: 8107 At special positions: 0 Unit cell: (81.76, 115.486, 125.706, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 1 15.00 O 1430 8.00 N 1346 7.00 C 5289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.40 Conformation dependent library (CDL) restraints added in 1.4 seconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 4 sheets defined 77.0% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 72 through 95 removed outlier: 4.245A pdb=" N LYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 4.096A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 4.012A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.656A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 210 through 220 removed outlier: 3.528A pdb=" N ALA A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.603A pdb=" N LYS A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 296 through 317 removed outlier: 3.607A pdb=" N THR A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.523A pdb=" N ALA A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 376 Processing helix chain 'A' and resid 377 through 380 Processing helix chain 'A' and resid 381 through 411 removed outlier: 3.886A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 removed outlier: 3.598A pdb=" N VAL A 423 " --> pdb=" O TRP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.676A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 469 removed outlier: 4.049A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 481 removed outlier: 5.127A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 513 removed outlier: 3.516A pdb=" N LYS A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 571 through 600 removed outlier: 3.688A pdb=" N ASP A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 620 removed outlier: 3.902A pdb=" N ASP A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 4.096A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N SER A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TRP A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 653 removed outlier: 3.613A pdb=" N ASP A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 706 removed outlier: 4.117A pdb=" N ILE A 684 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix removed outlier: 3.797A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP A 703 " --> pdb=" O PHE A 699 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LYS A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 755 removed outlier: 4.005A pdb=" N ILE A 734 " --> pdb=" O ASP A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.670A pdb=" N ILE A 759 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 783 Processing helix chain 'A' and resid 798 through 803 Processing helix chain 'A' and resid 803 through 812 removed outlier: 4.035A pdb=" N MET A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 858 removed outlier: 3.992A pdb=" N LEU A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Proline residue: A 819 - end of helix removed outlier: 3.572A pdb=" N LEU A 835 " --> pdb=" O ASN A 831 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.515A pdb=" N LEU A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 920 Processing helix chain 'A' and resid 925 through 942 removed outlier: 3.614A pdb=" N LYS A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 941 " --> pdb=" O LYS A 937 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET A 942 " --> pdb=" O MET A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 960 Processing helix chain 'A' and resid 966 through 975 Processing helix chain 'A' and resid 1043 through 1049 removed outlier: 3.992A pdb=" N VAL A1047 " --> pdb=" O GLY A1043 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A1048 " --> pdb=" O GLU A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1108 removed outlier: 3.657A pdb=" N ARG A1097 " --> pdb=" O VAL A1093 " (cutoff:3.500A) Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1123 removed outlier: 3.709A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1183 removed outlier: 4.066A pdb=" N GLU A1182 " --> pdb=" O THR A1179 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A1183 " --> pdb=" O ALA A1180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1179 through 1183' Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 981 removed outlier: 6.277A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.743A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 6.781A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1134 through 1136 577 hydrogen bonds defined for protein. 1701 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: 2.90 Time building geometry restraints manager: 3.71 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: 2536 1.34 - 1.46: 1089 1.46 - 1.58: 4564 1.58 - 1.70: 2 1.70 - 1.81: 76 Bond restraints: 8267 Sorted by residual: bond pdb=" C4 CMP A1401 " pdb=" C5 CMP A1401 " ideal model delta sigma weight residual 1.490 1.349 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C5 CMP A1401 " pdb=" C6 CMP A1401 " ideal model delta sigma weight residual 1.490 1.389 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C8 CMP A1401 " pdb=" N9 CMP A1401 " ideal model delta sigma weight residual 1.337 1.400 -0.063 2.00e-02 2.50e+03 9.83e+00 bond pdb=" C1' CMP A1401 " pdb=" O4' CMP A1401 " ideal model delta sigma weight residual 1.412 1.456 -0.044 1.50e-02 4.44e+03 8.50e+00 bond pdb=" O2P CMP A1401 " pdb=" P CMP A1401 " ideal model delta sigma weight residual 1.510 1.565 -0.055 2.00e-02 2.50e+03 7.47e+00 ... (remaining 8262 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.79: 214 106.79 - 113.75: 4815 113.75 - 120.72: 3624 120.72 - 127.68: 2479 127.68 - 134.64: 86 Bond angle restraints: 11218 Sorted by residual: angle pdb=" N TYR A 743 " pdb=" CA TYR A 743 " pdb=" C TYR A 743 " ideal model delta sigma weight residual 110.97 105.77 5.20 1.09e+00 8.42e-01 2.27e+01 angle pdb=" OD1 ASN A1040 " pdb=" CG ASN A1040 " pdb=" ND2 ASN A1040 " ideal model delta sigma weight residual 122.60 118.43 4.17 1.00e+00 1.00e+00 1.74e+01 angle pdb=" N GLY A1010 " pdb=" CA GLY A1010 " pdb=" C GLY A1010 " ideal model delta sigma weight residual 110.38 116.39 -6.01 1.48e+00 4.57e-01 1.65e+01 angle pdb=" N ALA A 964 " pdb=" CA ALA A 964 " pdb=" C ALA A 964 " ideal model delta sigma weight residual 111.71 116.14 -4.43 1.15e+00 7.56e-01 1.49e+01 angle pdb=" C ILE A 742 " pdb=" N TYR A 743 " pdb=" CA TYR A 743 " ideal model delta sigma weight residual 120.65 115.99 4.66 1.32e+00 5.74e-01 1.24e+01 ... (remaining 11213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.32: 4746 25.32 - 50.64: 168 50.64 - 75.96: 13 75.96 - 101.28: 2 101.28 - 126.61: 3 Dihedral angle restraints: 4932 sinusoidal: 1953 harmonic: 2979 Sorted by residual: dihedral pdb=" C3' CMP A1401 " pdb=" O3' CMP A1401 " pdb=" P CMP A1401 " pdb=" O1P CMP A1401 " ideal model delta sinusoidal sigma weight residual 300.00 173.39 126.61 1 2.00e+01 2.50e-03 3.83e+01 dihedral pdb=" C5' CMP A1401 " pdb=" O5' CMP A1401 " pdb=" P CMP A1401 " pdb=" O1P CMP A1401 " ideal model delta sinusoidal sigma weight residual 60.00 -173.83 -126.17 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" CA LEU A 963 " pdb=" C LEU A 963 " pdb=" N ALA A 964 " pdb=" CA ALA A 964 " ideal model delta harmonic sigma weight residual -180.00 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 4929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1062 0.048 - 0.097: 225 0.097 - 0.145: 50 0.145 - 0.194: 9 0.194 - 0.242: 2 Chirality restraints: 1348 Sorted by residual: chirality pdb=" CA THR A1049 " pdb=" N THR A1049 " pdb=" C THR A1049 " pdb=" CB THR A1049 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ARG A1097 " pdb=" N ARG A1097 " pdb=" C ARG A1097 " pdb=" CB ARG A1097 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LYS A1050 " pdb=" N LYS A1050 " pdb=" C LYS A1050 " pdb=" CB LYS A1050 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.82e-01 ... (remaining 1345 not shown) Planarity restraints: 1378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1009 " 0.069 2.00e-02 2.50e+03 3.48e-02 2.42e+01 pdb=" CG TYR A1009 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A1009 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A1009 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A1009 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A1009 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A1009 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A1009 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CMP A1401 " 0.049 2.00e-02 2.50e+03 2.51e-02 1.73e+01 pdb=" C2 CMP A1401 " -0.027 2.00e-02 2.50e+03 pdb=" C4 CMP A1401 " -0.009 2.00e-02 2.50e+03 pdb=" C5 CMP A1401 " -0.008 2.00e-02 2.50e+03 pdb=" C6 CMP A1401 " 0.003 2.00e-02 2.50e+03 pdb=" C8 CMP A1401 " -0.038 2.00e-02 2.50e+03 pdb=" N1 CMP A1401 " 0.001 2.00e-02 2.50e+03 pdb=" N3 CMP A1401 " -0.006 2.00e-02 2.50e+03 pdb=" N6 CMP A1401 " 0.044 2.00e-02 2.50e+03 pdb=" N7 CMP A1401 " -0.015 2.00e-02 2.50e+03 pdb=" N9 CMP A1401 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 962 " 0.033 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP A 962 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 962 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 962 " -0.042 2.00e-02 2.50e+03 pdb=" NE1 TRP A 962 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP A 962 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 962 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 962 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 962 " 0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP A 962 " 0.024 2.00e-02 2.50e+03 ... (remaining 1375 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 715 2.74 - 3.28: 8674 3.28 - 3.82: 13246 3.82 - 4.36: 14645 4.36 - 4.90: 25808 Nonbonded interactions: 63088 Sorted by model distance: nonbonded pdb=" O ILE A 81 " pdb=" OG SER A 84 " model vdw 2.197 2.440 nonbonded pdb=" OH TYR A 743 " pdb=" OD2 ASP A 767 " model vdw 2.268 2.440 nonbonded pdb=" OE2 GLU A 746 " pdb=" CD LYS A 750 " model vdw 2.327 3.440 nonbonded pdb=" O ASP A1078 " pdb=" OD1 ASP A1078 " model vdw 2.369 3.040 nonbonded pdb=" O ASP A 650 " pdb=" OG SER A 653 " model vdw 2.372 2.440 ... (remaining 63083 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.190 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 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 : 0.005 0.141 8267 Z= 0.307 Angle : 0.734 8.111 11218 Z= 0.449 Chirality : 0.043 0.242 1348 Planarity : 0.005 0.079 1378 Dihedral : 13.444 126.606 3000 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.11 % Allowed : 7.84 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.27), residues: 1012 helix: 1.91 (0.19), residues: 712 sheet: -0.90 (0.63), residues: 61 loop : 0.37 (0.44), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 962 HIS 0.002 0.000 HIS A 928 PHE 0.018 0.002 PHE A1032 TYR 0.069 0.002 TYR A1009 ARG 0.006 0.000 ARG A1053 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.6780 (mm) cc_final: 0.6556 (mt) REVERT: A 134 ASP cc_start: 0.7521 (m-30) cc_final: 0.6518 (p0) REVERT: A 149 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6673 (tm-30) REVERT: A 155 ASP cc_start: 0.6515 (t0) cc_final: 0.6081 (t0) REVERT: A 157 HIS cc_start: 0.6930 (m90) cc_final: 0.6287 (m-70) REVERT: A 160 MET cc_start: 0.7443 (mmt) cc_final: 0.6873 (mmt) REVERT: A 163 PHE cc_start: 0.7509 (t80) cc_final: 0.7250 (t80) REVERT: A 209 ASP cc_start: 0.7282 (t0) cc_final: 0.6839 (t0) REVERT: A 220 LEU cc_start: 0.7081 (mm) cc_final: 0.6809 (mt) REVERT: A 288 PHE cc_start: 0.7585 (t80) cc_final: 0.7038 (t80) REVERT: A 289 PHE cc_start: 0.7463 (m-80) cc_final: 0.7234 (m-10) REVERT: A 483 MET cc_start: 0.7348 (mtp) cc_final: 0.7109 (mtm) REVERT: A 485 ASP cc_start: 0.7754 (m-30) cc_final: 0.7395 (p0) REVERT: A 486 ILE cc_start: 0.7593 (mt) cc_final: 0.7276 (tp) REVERT: A 500 ARG cc_start: 0.7502 (tpp80) cc_final: 0.7196 (tpp80) REVERT: A 517 PHE cc_start: 0.6182 (m-80) cc_final: 0.5848 (m-80) REVERT: A 579 MET cc_start: 0.7017 (tmm) cc_final: 0.6714 (tmm) REVERT: A 580 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7568 (mm-30) REVERT: A 583 ARG cc_start: 0.7191 (ttp80) cc_final: 0.6800 (ttp80) REVERT: A 591 LYS cc_start: 0.7860 (mtpp) cc_final: 0.7521 (mttt) REVERT: A 606 GLU cc_start: 0.7031 (tp30) cc_final: 0.6538 (tp30) REVERT: A 609 ARG cc_start: 0.7824 (tpp80) cc_final: 0.6690 (tpp80) REVERT: A 613 GLN cc_start: 0.8122 (tt0) cc_final: 0.7559 (mt0) REVERT: A 616 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6686 (mt-10) REVERT: A 621 GLU cc_start: 0.6435 (mt-10) cc_final: 0.6029 (mt-10) REVERT: A 632 LYS cc_start: 0.7755 (ttmm) cc_final: 0.7523 (mttt) REVERT: A 810 MET cc_start: 0.6128 (mpp) cc_final: 0.5425 (mpp) REVERT: A 828 LYS cc_start: 0.7219 (mmmt) cc_final: 0.6955 (tppt) REVERT: A 859 ASP cc_start: 0.7459 (m-30) cc_final: 0.7176 (t0) REVERT: A 863 ILE cc_start: 0.6277 (mm) cc_final: 0.6042 (mm) REVERT: A 867 LEU cc_start: 0.6398 (mp) cc_final: 0.6078 (mt) REVERT: A 870 ILE cc_start: 0.6404 (mt) cc_final: 0.6084 (mm) REVERT: A 876 LEU cc_start: 0.6779 (mp) cc_final: 0.6568 (mm) REVERT: A 880 LYS cc_start: 0.7402 (tttt) cc_final: 0.7056 (ttpt) REVERT: A 887 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.6969 (mtp85) REVERT: A 915 GLU cc_start: 0.7240 (mt-10) cc_final: 0.7009 (mt-10) REVERT: A 926 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6769 (tt0) REVERT: A 938 MET cc_start: 0.7635 (tpp) cc_final: 0.7285 (ttt) REVERT: A 940 ARG cc_start: 0.7090 (mtt-85) cc_final: 0.6863 (mtm-85) REVERT: A 954 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7116 (mt-10) REVERT: A 966 ASP cc_start: 0.7310 (t0) cc_final: 0.6857 (p0) REVERT: A 967 MET cc_start: 0.7773 (mtm) cc_final: 0.7338 (mtm) REVERT: A 969 LEU cc_start: 0.8429 (tp) cc_final: 0.7889 (tp) REVERT: A 993 ASP cc_start: 0.6845 (m-30) cc_final: 0.6495 (t70) REVERT: A 994 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7590 (mt-10) REVERT: A 998 LEU cc_start: 0.6575 (mp) cc_final: 0.6345 (mp) REVERT: A 999 PHE cc_start: 0.7263 (m-80) cc_final: 0.7019 (m-80) REVERT: A 1033 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6429 (mt-10) REVERT: A 1035 TYR cc_start: 0.7867 (m-80) cc_final: 0.7454 (m-80) REVERT: A 1037 THR cc_start: 0.7432 (t) cc_final: 0.7070 (t) REVERT: A 1040 ASN cc_start: 0.7447 (m110) cc_final: 0.7100 (m110) REVERT: A 1042 ILE cc_start: 0.6463 (mt) cc_final: 0.6186 (tt) REVERT: A 1045 MET cc_start: 0.6961 (mtp) cc_final: 0.6721 (mtp) REVERT: A 1050 LYS cc_start: 0.7830 (mttt) cc_final: 0.7613 (mmmt) REVERT: A 1051 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7737 (ttmm) REVERT: A 1059 CYS cc_start: 0.6908 (m) cc_final: 0.6495 (m) REVERT: A 1061 THR cc_start: 0.7606 (p) cc_final: 0.7166 (p) REVERT: A 1071 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7935 (mt-10) REVERT: A 1073 MET cc_start: 0.7923 (mmm) cc_final: 0.7547 (mmp) REVERT: A 1085 SER cc_start: 0.8246 (t) cc_final: 0.7872 (m) REVERT: A 1098 ILE cc_start: 0.7594 (tp) cc_final: 0.7322 (tt) REVERT: A 1122 GLU cc_start: 0.7721 (tp30) cc_final: 0.7521 (mm-30) REVERT: A 1168 SER cc_start: 0.7593 (t) cc_final: 0.7248 (p) REVERT: A 1183 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7077 (mm-30) outliers start: 1 outliers final: 0 residues processed: 309 average time/residue: 0.2345 time to fit residues: 93.7496 Evaluate side-chains 264 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 0.0030 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN A 889 HIS A 900 GLN A1054 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8267 Z= 0.204 Angle : 0.564 8.687 11218 Z= 0.293 Chirality : 0.040 0.156 1348 Planarity : 0.004 0.037 1378 Dihedral : 8.320 145.017 1104 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.50 % Allowed : 13.98 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.27), residues: 1012 helix: 2.14 (0.19), residues: 710 sheet: -0.78 (0.64), residues: 61 loop : 0.74 (0.46), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 962 HIS 0.003 0.001 HIS A 869 PHE 0.026 0.002 PHE A 739 TYR 0.018 0.001 TYR A 984 ARG 0.006 0.000 ARG A 990 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 255 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.6951 (mm) cc_final: 0.6634 (mt) REVERT: A 133 MET cc_start: 0.6691 (mmt) cc_final: 0.5944 (mmt) REVERT: A 134 ASP cc_start: 0.7541 (m-30) cc_final: 0.6475 (p0) REVERT: A 149 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6642 (tm-30) REVERT: A 155 ASP cc_start: 0.6010 (t0) cc_final: 0.5587 (t0) REVERT: A 157 HIS cc_start: 0.6830 (m90) cc_final: 0.6436 (m-70) REVERT: A 160 MET cc_start: 0.7421 (mmt) cc_final: 0.6888 (mmt) REVERT: A 174 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5987 (tp) REVERT: A 209 ASP cc_start: 0.7318 (t0) cc_final: 0.6781 (t0) REVERT: A 238 ASP cc_start: 0.6045 (m-30) cc_final: 0.5818 (m-30) REVERT: A 443 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6964 (tm-30) REVERT: A 475 GLN cc_start: 0.7590 (tp40) cc_final: 0.7260 (tp-100) REVERT: A 485 ASP cc_start: 0.7789 (m-30) cc_final: 0.7373 (p0) REVERT: A 486 ILE cc_start: 0.7848 (mt) cc_final: 0.7492 (tp) REVERT: A 500 ARG cc_start: 0.7525 (tpp80) cc_final: 0.7220 (tpp80) REVERT: A 579 MET cc_start: 0.6970 (tmm) cc_final: 0.6678 (tmm) REVERT: A 580 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7649 (mm-30) REVERT: A 583 ARG cc_start: 0.7417 (ttp80) cc_final: 0.7093 (ttp80) REVERT: A 588 LYS cc_start: 0.7569 (ttpp) cc_final: 0.7158 (ttpp) REVERT: A 591 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7619 (mtpt) REVERT: A 609 ARG cc_start: 0.7807 (tpp80) cc_final: 0.6666 (tpp80) REVERT: A 613 GLN cc_start: 0.8108 (tt0) cc_final: 0.7544 (mt0) REVERT: A 628 VAL cc_start: 0.7532 (p) cc_final: 0.7014 (m) REVERT: A 643 TRP cc_start: 0.7533 (t60) cc_final: 0.7121 (t60) REVERT: A 810 MET cc_start: 0.6337 (OUTLIER) cc_final: 0.5860 (mpp) REVERT: A 856 ARG cc_start: 0.6912 (ptp90) cc_final: 0.6035 (ptp90) REVERT: A 859 ASP cc_start: 0.7671 (m-30) cc_final: 0.7361 (t0) REVERT: A 863 ILE cc_start: 0.6248 (mm) cc_final: 0.5993 (mm) REVERT: A 872 GLU cc_start: 0.6815 (mm-30) cc_final: 0.5964 (mm-30) REVERT: A 876 LEU cc_start: 0.6849 (mp) cc_final: 0.6599 (mm) REVERT: A 880 LYS cc_start: 0.7349 (tttt) cc_final: 0.7005 (ttpp) REVERT: A 911 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6750 (mm-30) REVERT: A 915 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6958 (mt-10) REVERT: A 926 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6715 (tt0) REVERT: A 938 MET cc_start: 0.7683 (tpp) cc_final: 0.7341 (ttm) REVERT: A 946 SER cc_start: 0.8052 (p) cc_final: 0.7426 (t) REVERT: A 966 ASP cc_start: 0.7296 (t0) cc_final: 0.6838 (t0) REVERT: A 968 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7671 (mtmt) REVERT: A 991 GLU cc_start: 0.8019 (tt0) cc_final: 0.7440 (tp30) REVERT: A 993 ASP cc_start: 0.6923 (m-30) cc_final: 0.6708 (m-30) REVERT: A 1035 TYR cc_start: 0.8034 (m-80) cc_final: 0.7832 (m-80) REVERT: A 1044 GLU cc_start: 0.7370 (tt0) cc_final: 0.7113 (tp30) REVERT: A 1050 LYS cc_start: 0.7512 (mttt) cc_final: 0.7283 (mmmt) REVERT: A 1071 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8016 (mp0) REVERT: A 1085 SER cc_start: 0.8198 (t) cc_final: 0.7940 (m) REVERT: A 1105 GLU cc_start: 0.8186 (tt0) cc_final: 0.7390 (pp20) REVERT: A 1109 PHE cc_start: 0.8161 (m-10) cc_final: 0.7939 (m-10) REVERT: A 1122 GLU cc_start: 0.7675 (tp30) cc_final: 0.7334 (mm-30) REVERT: A 1142 LEU cc_start: 0.7111 (tp) cc_final: 0.6882 (mt) REVERT: A 1183 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7005 (mm-30) REVERT: A 1190 ARG cc_start: 0.6945 (mmt180) cc_final: 0.6549 (mmm-85) outliers start: 22 outliers final: 10 residues processed: 265 average time/residue: 0.2352 time to fit residues: 81.2630 Evaluate side-chains 254 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 242 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1129 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 900 GLN A1149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8267 Z= 0.273 Angle : 0.559 8.900 11218 Z= 0.293 Chirality : 0.040 0.154 1348 Planarity : 0.004 0.043 1378 Dihedral : 8.264 143.871 1104 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.64 % Allowed : 16.70 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.04 (0.27), residues: 1012 helix: 1.87 (0.19), residues: 718 sheet: -0.58 (0.75), residues: 54 loop : 0.40 (0.44), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 962 HIS 0.003 0.001 HIS A 869 PHE 0.025 0.002 PHE A 739 TYR 0.013 0.001 TYR A1066 ARG 0.007 0.001 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 250 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.6967 (mm) cc_final: 0.6668 (mt) REVERT: A 133 MET cc_start: 0.6649 (mmt) cc_final: 0.5886 (mmt) REVERT: A 134 ASP cc_start: 0.7521 (m-30) cc_final: 0.6458 (p0) REVERT: A 155 ASP cc_start: 0.5983 (t0) cc_final: 0.5449 (t0) REVERT: A 157 HIS cc_start: 0.6879 (m90) cc_final: 0.6480 (m-70) REVERT: A 160 MET cc_start: 0.7482 (mmt) cc_final: 0.7006 (mmt) REVERT: A 205 MET cc_start: 0.7359 (tpp) cc_final: 0.6696 (mmm) REVERT: A 209 ASP cc_start: 0.7386 (t0) cc_final: 0.6784 (t0) REVERT: A 216 LEU cc_start: 0.7209 (mt) cc_final: 0.7004 (mp) REVERT: A 238 ASP cc_start: 0.6111 (m-30) cc_final: 0.5836 (m-30) REVERT: A 383 MET cc_start: 0.7395 (mmm) cc_final: 0.7109 (tpp) REVERT: A 443 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6915 (tm-30) REVERT: A 475 GLN cc_start: 0.7531 (tp40) cc_final: 0.6996 (tp-100) REVERT: A 485 ASP cc_start: 0.7839 (m-30) cc_final: 0.7491 (p0) REVERT: A 500 ARG cc_start: 0.7544 (tpp80) cc_final: 0.7228 (tpp80) REVERT: A 588 LYS cc_start: 0.7605 (ttpp) cc_final: 0.7151 (ttpp) REVERT: A 591 LYS cc_start: 0.7846 (mtpp) cc_final: 0.7567 (mtpt) REVERT: A 599 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7038 (mt-10) REVERT: A 616 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7356 (mm-30) REVERT: A 630 ASP cc_start: 0.7834 (m-30) cc_final: 0.7447 (m-30) REVERT: A 643 TRP cc_start: 0.7588 (t60) cc_final: 0.7052 (t60) REVERT: A 644 LEU cc_start: 0.7272 (mt) cc_final: 0.7000 (mm) REVERT: A 705 MET cc_start: 0.3020 (mmt) cc_final: 0.2727 (mmm) REVERT: A 810 MET cc_start: 0.6521 (OUTLIER) cc_final: 0.5995 (mpp) REVERT: A 857 MET cc_start: 0.7461 (tpp) cc_final: 0.7254 (tpp) REVERT: A 859 ASP cc_start: 0.7639 (m-30) cc_final: 0.7431 (t0) REVERT: A 863 ILE cc_start: 0.6364 (mm) cc_final: 0.5945 (mm) REVERT: A 866 GLU cc_start: 0.6464 (tm-30) cc_final: 0.6245 (tm-30) REVERT: A 872 GLU cc_start: 0.6814 (mm-30) cc_final: 0.5911 (mm-30) REVERT: A 876 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6568 (mm) REVERT: A 880 LYS cc_start: 0.7397 (tttt) cc_final: 0.7014 (ttpt) REVERT: A 887 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.7304 (mtp85) REVERT: A 911 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6760 (mm-30) REVERT: A 915 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6965 (mt-10) REVERT: A 938 MET cc_start: 0.7845 (tpp) cc_final: 0.7426 (ttm) REVERT: A 946 SER cc_start: 0.8008 (p) cc_final: 0.7339 (t) REVERT: A 966 ASP cc_start: 0.7346 (t0) cc_final: 0.6980 (t0) REVERT: A 986 GLU cc_start: 0.6141 (tt0) cc_final: 0.5880 (tt0) REVERT: A 991 GLU cc_start: 0.8136 (tt0) cc_final: 0.7537 (tp30) REVERT: A 994 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7478 (tm-30) REVERT: A 998 LEU cc_start: 0.6498 (mp) cc_final: 0.6285 (mp) REVERT: A 1035 TYR cc_start: 0.7973 (m-80) cc_final: 0.7758 (m-80) REVERT: A 1071 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7971 (tm-30) REVERT: A 1085 SER cc_start: 0.8239 (t) cc_final: 0.7808 (p) REVERT: A 1105 GLU cc_start: 0.8207 (tt0) cc_final: 0.7401 (pp20) REVERT: A 1109 PHE cc_start: 0.8180 (m-10) cc_final: 0.7948 (m-10) REVERT: A 1122 GLU cc_start: 0.7762 (tp30) cc_final: 0.7457 (mm-30) REVERT: A 1190 ARG cc_start: 0.7121 (mmt180) cc_final: 0.6719 (mmm160) outliers start: 32 outliers final: 22 residues processed: 261 average time/residue: 0.2178 time to fit residues: 74.9385 Evaluate side-chains 265 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 241 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 0.0870 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A1120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8267 Z= 0.219 Angle : 0.548 8.842 11218 Z= 0.280 Chirality : 0.040 0.180 1348 Planarity : 0.004 0.042 1378 Dihedral : 8.235 144.268 1104 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.86 % Allowed : 17.27 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.27), residues: 1012 helix: 1.88 (0.19), residues: 719 sheet: -0.44 (0.75), residues: 54 loop : 0.16 (0.42), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 962 HIS 0.003 0.001 HIS A 869 PHE 0.017 0.001 PHE A 739 TYR 0.016 0.001 TYR A 984 ARG 0.005 0.000 ARG A 990 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 244 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6015 (mptt) cc_final: 0.5804 (mppt) REVERT: A 108 ILE cc_start: 0.6960 (mm) cc_final: 0.6669 (mt) REVERT: A 134 ASP cc_start: 0.7499 (m-30) cc_final: 0.6414 (p0) REVERT: A 155 ASP cc_start: 0.6033 (t0) cc_final: 0.5430 (t0) REVERT: A 157 HIS cc_start: 0.6841 (m90) cc_final: 0.6459 (m90) REVERT: A 160 MET cc_start: 0.7534 (mmt) cc_final: 0.7043 (mmt) REVERT: A 174 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5926 (tp) REVERT: A 199 MET cc_start: 0.7442 (mmm) cc_final: 0.6772 (tpp) REVERT: A 205 MET cc_start: 0.7231 (tpp) cc_final: 0.6783 (mmm) REVERT: A 209 ASP cc_start: 0.7373 (t0) cc_final: 0.6793 (t70) REVERT: A 238 ASP cc_start: 0.6032 (m-30) cc_final: 0.5720 (m-30) REVERT: A 383 MET cc_start: 0.7393 (mmm) cc_final: 0.7151 (tpp) REVERT: A 443 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6951 (tm-30) REVERT: A 475 GLN cc_start: 0.7431 (tp40) cc_final: 0.7025 (tp40) REVERT: A 485 ASP cc_start: 0.7847 (m-30) cc_final: 0.7470 (p0) REVERT: A 500 ARG cc_start: 0.7534 (tpp80) cc_final: 0.7218 (tpp80) REVERT: A 579 MET cc_start: 0.7105 (tmm) cc_final: 0.6765 (tmm) REVERT: A 580 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7635 (mm-30) REVERT: A 583 ARG cc_start: 0.7493 (tmm-80) cc_final: 0.6892 (ttp80) REVERT: A 585 ARG cc_start: 0.7464 (ttm-80) cc_final: 0.7042 (ttp-170) REVERT: A 588 LYS cc_start: 0.7568 (ttpp) cc_final: 0.7113 (ttpp) REVERT: A 591 LYS cc_start: 0.7827 (mtpp) cc_final: 0.7591 (mtpt) REVERT: A 616 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7511 (mm-30) REVERT: A 630 ASP cc_start: 0.7843 (m-30) cc_final: 0.7439 (m-30) REVERT: A 643 TRP cc_start: 0.7582 (t60) cc_final: 0.7059 (t60) REVERT: A 644 LEU cc_start: 0.7260 (mt) cc_final: 0.7012 (mm) REVERT: A 705 MET cc_start: 0.2930 (mmt) cc_final: 0.2432 (mmm) REVERT: A 810 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.6025 (mpp) REVERT: A 815 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7180 (ttpp) REVERT: A 863 ILE cc_start: 0.6288 (mm) cc_final: 0.5916 (mm) REVERT: A 866 GLU cc_start: 0.6485 (tm-30) cc_final: 0.6256 (tm-30) REVERT: A 872 GLU cc_start: 0.6813 (mm-30) cc_final: 0.5945 (mm-30) REVERT: A 876 LEU cc_start: 0.6805 (mp) cc_final: 0.6566 (mm) REVERT: A 880 LYS cc_start: 0.7472 (tttt) cc_final: 0.7067 (ttpt) REVERT: A 887 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.7284 (mtp85) REVERT: A 900 GLN cc_start: 0.7453 (mt0) cc_final: 0.7188 (mm-40) REVERT: A 911 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6800 (mm-30) REVERT: A 915 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6939 (mt-10) REVERT: A 938 MET cc_start: 0.7906 (tpp) cc_final: 0.7518 (ttm) REVERT: A 946 SER cc_start: 0.8031 (p) cc_final: 0.7297 (t) REVERT: A 966 ASP cc_start: 0.7341 (t0) cc_final: 0.6896 (t0) REVERT: A 968 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7785 (mtmt) REVERT: A 986 GLU cc_start: 0.6201 (tt0) cc_final: 0.5573 (tt0) REVERT: A 991 GLU cc_start: 0.8145 (tt0) cc_final: 0.7515 (tp30) REVERT: A 994 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7446 (tm-30) REVERT: A 998 LEU cc_start: 0.6531 (mp) cc_final: 0.6291 (mp) REVERT: A 1035 TYR cc_start: 0.7977 (m-80) cc_final: 0.7743 (m-80) REVERT: A 1071 GLU cc_start: 0.8229 (mt-10) cc_final: 0.8013 (mp0) REVERT: A 1085 SER cc_start: 0.8228 (t) cc_final: 0.7817 (p) REVERT: A 1105 GLU cc_start: 0.8219 (tt0) cc_final: 0.7424 (pp20) REVERT: A 1110 GLN cc_start: 0.7760 (mp10) cc_final: 0.7514 (mp10) REVERT: A 1122 GLU cc_start: 0.7770 (tp30) cc_final: 0.7455 (mm-30) REVERT: A 1145 VAL cc_start: 0.7984 (t) cc_final: 0.7743 (p) REVERT: A 1190 ARG cc_start: 0.6984 (mmt180) cc_final: 0.6728 (mmm-85) outliers start: 34 outliers final: 25 residues processed: 256 average time/residue: 0.2220 time to fit residues: 75.0776 Evaluate side-chains 265 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 237 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 815 LYS Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8267 Z= 0.217 Angle : 0.536 8.812 11218 Z= 0.276 Chirality : 0.039 0.143 1348 Planarity : 0.004 0.044 1378 Dihedral : 8.223 144.471 1104 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.55 % Allowed : 17.16 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.27), residues: 1012 helix: 1.88 (0.19), residues: 722 sheet: -0.56 (0.74), residues: 54 loop : -0.03 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 635 HIS 0.003 0.001 HIS A1120 PHE 0.021 0.001 PHE A 598 TYR 0.014 0.001 TYR A 984 ARG 0.005 0.000 ARG A 856 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 239 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6025 (mptt) cc_final: 0.5802 (mppt) REVERT: A 108 ILE cc_start: 0.6955 (mm) cc_final: 0.6669 (mt) REVERT: A 134 ASP cc_start: 0.7498 (m-30) cc_final: 0.6473 (p0) REVERT: A 149 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6528 (tm-30) REVERT: A 155 ASP cc_start: 0.6048 (t0) cc_final: 0.5467 (t0) REVERT: A 157 HIS cc_start: 0.6814 (m90) cc_final: 0.6391 (m90) REVERT: A 160 MET cc_start: 0.7538 (mmt) cc_final: 0.7054 (mmt) REVERT: A 168 ILE cc_start: 0.6737 (tt) cc_final: 0.6343 (pt) REVERT: A 199 MET cc_start: 0.7489 (mmm) cc_final: 0.6838 (tpp) REVERT: A 205 MET cc_start: 0.7137 (tpp) cc_final: 0.6758 (mmm) REVERT: A 209 ASP cc_start: 0.7351 (t0) cc_final: 0.6783 (t70) REVERT: A 238 ASP cc_start: 0.6103 (m-30) cc_final: 0.5755 (m-30) REVERT: A 373 THR cc_start: 0.6805 (m) cc_final: 0.6599 (m) REVERT: A 383 MET cc_start: 0.7394 (mmm) cc_final: 0.7170 (tpp) REVERT: A 424 ILE cc_start: 0.6733 (mm) cc_final: 0.6507 (tp) REVERT: A 443 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6932 (tm-30) REVERT: A 475 GLN cc_start: 0.7363 (tp40) cc_final: 0.6957 (tp40) REVERT: A 485 ASP cc_start: 0.7849 (m-30) cc_final: 0.7482 (p0) REVERT: A 500 ARG cc_start: 0.7515 (tpp80) cc_final: 0.7194 (tpp80) REVERT: A 585 ARG cc_start: 0.7346 (ttm-80) cc_final: 0.6977 (ttp-170) REVERT: A 588 LYS cc_start: 0.7576 (ttpp) cc_final: 0.7123 (ttpp) REVERT: A 591 LYS cc_start: 0.7841 (mtpp) cc_final: 0.7611 (mtpt) REVERT: A 599 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6843 (mt-10) REVERT: A 616 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7512 (mm-30) REVERT: A 630 ASP cc_start: 0.7846 (m-30) cc_final: 0.7456 (m-30) REVERT: A 643 TRP cc_start: 0.7589 (t60) cc_final: 0.7074 (t60) REVERT: A 644 LEU cc_start: 0.7256 (mt) cc_final: 0.7041 (mm) REVERT: A 705 MET cc_start: 0.2883 (mmt) cc_final: 0.2488 (mmt) REVERT: A 810 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6105 (mpp) REVERT: A 815 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7222 (ttpp) REVERT: A 856 ARG cc_start: 0.7204 (ptp90) cc_final: 0.6898 (ptt180) REVERT: A 863 ILE cc_start: 0.6267 (mm) cc_final: 0.5809 (mm) REVERT: A 866 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6280 (tm-30) REVERT: A 872 GLU cc_start: 0.6816 (mm-30) cc_final: 0.5947 (mm-30) REVERT: A 876 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6600 (mm) REVERT: A 880 LYS cc_start: 0.7483 (tttt) cc_final: 0.7090 (ttpt) REVERT: A 887 ARG cc_start: 0.7609 (mmm-85) cc_final: 0.7324 (mtp85) REVERT: A 911 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6796 (mm-30) REVERT: A 915 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6923 (mt-10) REVERT: A 938 MET cc_start: 0.7949 (tpp) cc_final: 0.7550 (ttm) REVERT: A 946 SER cc_start: 0.8027 (p) cc_final: 0.7265 (t) REVERT: A 986 GLU cc_start: 0.6215 (tt0) cc_final: 0.5576 (tt0) REVERT: A 991 GLU cc_start: 0.8130 (tt0) cc_final: 0.7610 (tp30) REVERT: A 1035 TYR cc_start: 0.7969 (m-80) cc_final: 0.7738 (m-80) REVERT: A 1071 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7989 (mp0) REVERT: A 1082 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6292 (tt) REVERT: A 1085 SER cc_start: 0.8270 (t) cc_final: 0.7840 (p) REVERT: A 1105 GLU cc_start: 0.8169 (tt0) cc_final: 0.7413 (pp20) REVERT: A 1118 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7087 (mtmm) REVERT: A 1122 GLU cc_start: 0.7759 (tp30) cc_final: 0.7456 (mm-30) REVERT: A 1145 VAL cc_start: 0.7983 (t) cc_final: 0.7725 (p) REVERT: A 1190 ARG cc_start: 0.6936 (mmt180) cc_final: 0.6498 (mmm-85) outliers start: 40 outliers final: 25 residues processed: 254 average time/residue: 0.2145 time to fit residues: 72.3199 Evaluate side-chains 268 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 238 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 815 LYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1118 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 98 optimal weight: 0.0970 chunk 81 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8267 Z= 0.193 Angle : 0.527 8.765 11218 Z= 0.271 Chirality : 0.039 0.181 1348 Planarity : 0.004 0.044 1378 Dihedral : 8.203 145.168 1104 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 5.00 % Allowed : 16.82 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.27), residues: 1012 helix: 2.00 (0.20), residues: 717 sheet: -0.63 (0.74), residues: 54 loop : -0.11 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 635 HIS 0.003 0.001 HIS A1120 PHE 0.018 0.001 PHE A 598 TYR 0.015 0.001 TYR A 984 ARG 0.005 0.000 ARG A 812 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 243 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.6948 (mm) cc_final: 0.6658 (mt) REVERT: A 134 ASP cc_start: 0.7494 (m-30) cc_final: 0.6425 (p0) REVERT: A 149 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6447 (tm-30) REVERT: A 155 ASP cc_start: 0.6051 (t0) cc_final: 0.5410 (t0) REVERT: A 157 HIS cc_start: 0.6794 (m90) cc_final: 0.6268 (m-70) REVERT: A 160 MET cc_start: 0.7534 (mmt) cc_final: 0.7051 (mmt) REVERT: A 199 MET cc_start: 0.7452 (mmm) cc_final: 0.6768 (tpp) REVERT: A 238 ASP cc_start: 0.6188 (m-30) cc_final: 0.5841 (m-30) REVERT: A 383 MET cc_start: 0.7376 (mmm) cc_final: 0.7159 (tpp) REVERT: A 424 ILE cc_start: 0.6739 (mm) cc_final: 0.6521 (tp) REVERT: A 443 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6938 (tm-30) REVERT: A 475 GLN cc_start: 0.7380 (tp40) cc_final: 0.6881 (tp-100) REVERT: A 485 ASP cc_start: 0.7865 (m-30) cc_final: 0.7471 (p0) REVERT: A 500 ARG cc_start: 0.7514 (tpp80) cc_final: 0.7199 (tpp80) REVERT: A 583 ARG cc_start: 0.7857 (tmm160) cc_final: 0.7554 (tmm-80) REVERT: A 588 LYS cc_start: 0.7568 (ttpp) cc_final: 0.7117 (ttpp) REVERT: A 591 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7581 (mtpt) REVERT: A 616 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7405 (mm-30) REVERT: A 621 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7054 (mm-30) REVERT: A 624 GLN cc_start: 0.7622 (tp-100) cc_final: 0.7309 (tp40) REVERT: A 630 ASP cc_start: 0.7858 (m-30) cc_final: 0.7441 (m-30) REVERT: A 643 TRP cc_start: 0.7582 (t60) cc_final: 0.7072 (t60) REVERT: A 705 MET cc_start: 0.2857 (mmt) cc_final: 0.2477 (mmt) REVERT: A 810 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.5955 (mpp) REVERT: A 815 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7259 (ttpp) REVERT: A 856 ARG cc_start: 0.7215 (ptp90) cc_final: 0.6370 (ptt180) REVERT: A 863 ILE cc_start: 0.6233 (mm) cc_final: 0.5761 (mm) REVERT: A 866 GLU cc_start: 0.6534 (tm-30) cc_final: 0.6251 (tm-30) REVERT: A 872 GLU cc_start: 0.6836 (mm-30) cc_final: 0.5904 (mm-30) REVERT: A 876 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6621 (mm) REVERT: A 880 LYS cc_start: 0.7501 (tttt) cc_final: 0.7090 (ttpt) REVERT: A 887 ARG cc_start: 0.7617 (mmm-85) cc_final: 0.7352 (mtp85) REVERT: A 911 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6796 (mm-30) REVERT: A 915 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6921 (mt-10) REVERT: A 938 MET cc_start: 0.7938 (tpp) cc_final: 0.7561 (ttm) REVERT: A 946 SER cc_start: 0.8041 (p) cc_final: 0.7259 (t) REVERT: A 960 VAL cc_start: 0.6649 (OUTLIER) cc_final: 0.6395 (p) REVERT: A 966 ASP cc_start: 0.7372 (t0) cc_final: 0.6524 (p0) REVERT: A 986 GLU cc_start: 0.6270 (tt0) cc_final: 0.5614 (tt0) REVERT: A 991 GLU cc_start: 0.8142 (tt0) cc_final: 0.7610 (tp30) REVERT: A 1035 TYR cc_start: 0.7968 (m-80) cc_final: 0.7715 (m-80) REVERT: A 1082 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6350 (tt) REVERT: A 1085 SER cc_start: 0.8279 (t) cc_final: 0.7847 (p) REVERT: A 1105 GLU cc_start: 0.8102 (tt0) cc_final: 0.7268 (pp20) REVERT: A 1107 MET cc_start: 0.6308 (ttm) cc_final: 0.6103 (ttm) REVERT: A 1109 PHE cc_start: 0.8145 (m-10) cc_final: 0.7654 (m-80) REVERT: A 1110 GLN cc_start: 0.7879 (mp10) cc_final: 0.7301 (mp10) REVERT: A 1122 GLU cc_start: 0.7769 (tp30) cc_final: 0.7435 (mm-30) REVERT: A 1145 VAL cc_start: 0.7980 (t) cc_final: 0.7732 (p) outliers start: 44 outliers final: 28 residues processed: 260 average time/residue: 0.2282 time to fit residues: 78.3503 Evaluate side-chains 271 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 238 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 815 LYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 0.0170 chunk 98 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8267 Z= 0.205 Angle : 0.534 8.746 11218 Z= 0.274 Chirality : 0.039 0.158 1348 Planarity : 0.004 0.043 1378 Dihedral : 8.202 145.237 1104 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.20 % Allowed : 18.41 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.27), residues: 1012 helix: 2.00 (0.19), residues: 717 sheet: -0.67 (0.74), residues: 54 loop : -0.10 (0.43), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 595 HIS 0.003 0.001 HIS A 157 PHE 0.017 0.001 PHE A 598 TYR 0.013 0.001 TYR A 984 ARG 0.005 0.000 ARG A 812 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 244 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.6940 (mm) cc_final: 0.6648 (mt) REVERT: A 134 ASP cc_start: 0.7463 (m-30) cc_final: 0.6447 (p0) REVERT: A 149 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6431 (tm-30) REVERT: A 155 ASP cc_start: 0.6141 (t0) cc_final: 0.5523 (t70) REVERT: A 157 HIS cc_start: 0.6770 (m90) cc_final: 0.6359 (m90) REVERT: A 160 MET cc_start: 0.7533 (mmt) cc_final: 0.7044 (mmt) REVERT: A 168 ILE cc_start: 0.6729 (tt) cc_final: 0.6348 (pt) REVERT: A 199 MET cc_start: 0.7466 (mmm) cc_final: 0.6781 (tpp) REVERT: A 238 ASP cc_start: 0.6209 (m-30) cc_final: 0.5881 (m-30) REVERT: A 383 MET cc_start: 0.7387 (mmm) cc_final: 0.7163 (tpp) REVERT: A 424 ILE cc_start: 0.6717 (mm) cc_final: 0.6500 (tp) REVERT: A 443 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6933 (tm-30) REVERT: A 475 GLN cc_start: 0.7378 (tp40) cc_final: 0.6891 (tp-100) REVERT: A 485 ASP cc_start: 0.7865 (m-30) cc_final: 0.7469 (p0) REVERT: A 500 ARG cc_start: 0.7510 (tpp80) cc_final: 0.7205 (tpp80) REVERT: A 573 ARG cc_start: 0.6995 (tpp80) cc_final: 0.6609 (tpp80) REVERT: A 583 ARG cc_start: 0.7904 (tmm160) cc_final: 0.7600 (tmm-80) REVERT: A 588 LYS cc_start: 0.7568 (ttpp) cc_final: 0.7124 (ttpp) REVERT: A 591 LYS cc_start: 0.7829 (mtpp) cc_final: 0.7514 (mtpt) REVERT: A 602 MET cc_start: 0.7291 (mmm) cc_final: 0.7037 (tpp) REVERT: A 616 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7351 (mm-30) REVERT: A 624 GLN cc_start: 0.7607 (tp-100) cc_final: 0.7401 (tp40) REVERT: A 630 ASP cc_start: 0.7860 (m-30) cc_final: 0.7414 (m-30) REVERT: A 643 TRP cc_start: 0.7736 (t60) cc_final: 0.7315 (t60) REVERT: A 810 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.5910 (mpp) REVERT: A 847 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6854 (mm-30) REVERT: A 856 ARG cc_start: 0.7241 (ptp90) cc_final: 0.6269 (ptt180) REVERT: A 863 ILE cc_start: 0.6198 (mm) cc_final: 0.5816 (mm) REVERT: A 866 GLU cc_start: 0.6546 (tm-30) cc_final: 0.6254 (tm-30) REVERT: A 872 GLU cc_start: 0.6753 (mm-30) cc_final: 0.5946 (mm-30) REVERT: A 877 GLN cc_start: 0.7304 (tt0) cc_final: 0.6816 (tt0) REVERT: A 880 LYS cc_start: 0.7494 (tttt) cc_final: 0.7066 (ttpt) REVERT: A 887 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7333 (mtp85) REVERT: A 911 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6791 (mm-30) REVERT: A 915 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6910 (mt-10) REVERT: A 938 MET cc_start: 0.7936 (tpp) cc_final: 0.7557 (ttm) REVERT: A 946 SER cc_start: 0.8051 (p) cc_final: 0.7271 (t) REVERT: A 960 VAL cc_start: 0.6619 (OUTLIER) cc_final: 0.6360 (p) REVERT: A 966 ASP cc_start: 0.7316 (t0) cc_final: 0.6502 (p0) REVERT: A 986 GLU cc_start: 0.6279 (tt0) cc_final: 0.5621 (tt0) REVERT: A 991 GLU cc_start: 0.8172 (tt0) cc_final: 0.7601 (tp30) REVERT: A 1035 TYR cc_start: 0.7963 (m-80) cc_final: 0.7712 (m-80) REVERT: A 1082 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6385 (tt) REVERT: A 1085 SER cc_start: 0.8307 (t) cc_final: 0.7881 (p) REVERT: A 1105 GLU cc_start: 0.8158 (tt0) cc_final: 0.7320 (pp20) REVERT: A 1109 PHE cc_start: 0.8131 (m-10) cc_final: 0.7649 (m-80) REVERT: A 1110 GLN cc_start: 0.7894 (mp10) cc_final: 0.7257 (mp10) REVERT: A 1122 GLU cc_start: 0.7720 (tp30) cc_final: 0.7405 (mm-30) REVERT: A 1145 VAL cc_start: 0.7960 (t) cc_final: 0.7699 (p) REVERT: A 1190 ARG cc_start: 0.6887 (mmt180) cc_final: 0.6664 (mmm-85) outliers start: 37 outliers final: 26 residues processed: 260 average time/residue: 0.2217 time to fit residues: 75.8950 Evaluate side-chains 267 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 238 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8267 Z= 0.256 Angle : 0.573 8.739 11218 Z= 0.293 Chirality : 0.040 0.147 1348 Planarity : 0.004 0.046 1378 Dihedral : 8.210 144.898 1104 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.52 % Allowed : 20.00 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.27), residues: 1012 helix: 1.87 (0.19), residues: 717 sheet: -0.67 (0.74), residues: 54 loop : -0.14 (0.43), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 595 HIS 0.004 0.001 HIS A1120 PHE 0.017 0.002 PHE A 598 TYR 0.011 0.001 TYR A 743 ARG 0.005 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 236 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.6938 (mm) cc_final: 0.6644 (mt) REVERT: A 134 ASP cc_start: 0.7479 (m-30) cc_final: 0.6446 (p0) REVERT: A 155 ASP cc_start: 0.6194 (t0) cc_final: 0.5554 (t70) REVERT: A 157 HIS cc_start: 0.6784 (m90) cc_final: 0.6393 (m90) REVERT: A 160 MET cc_start: 0.7516 (mmt) cc_final: 0.7281 (mmt) REVERT: A 164 SER cc_start: 0.7560 (m) cc_final: 0.7275 (p) REVERT: A 168 ILE cc_start: 0.6750 (tt) cc_final: 0.6377 (pt) REVERT: A 209 ASP cc_start: 0.7362 (t0) cc_final: 0.6940 (t0) REVERT: A 219 ASP cc_start: 0.7419 (t0) cc_final: 0.7180 (t0) REVERT: A 238 ASP cc_start: 0.6214 (m-30) cc_final: 0.5930 (m-30) REVERT: A 383 MET cc_start: 0.7403 (mmm) cc_final: 0.7181 (tpp) REVERT: A 424 ILE cc_start: 0.6737 (mm) cc_final: 0.6503 (tp) REVERT: A 443 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6946 (tm-30) REVERT: A 475 GLN cc_start: 0.7377 (tp40) cc_final: 0.6884 (tp-100) REVERT: A 485 ASP cc_start: 0.7886 (m-30) cc_final: 0.7462 (p0) REVERT: A 500 ARG cc_start: 0.7513 (tpp80) cc_final: 0.7201 (tpp80) REVERT: A 573 ARG cc_start: 0.7035 (tpp80) cc_final: 0.6630 (tpp80) REVERT: A 583 ARG cc_start: 0.7917 (tmm160) cc_final: 0.7670 (tmm-80) REVERT: A 585 ARG cc_start: 0.7303 (ttm-80) cc_final: 0.6931 (ttp-170) REVERT: A 588 LYS cc_start: 0.7577 (ttpp) cc_final: 0.7133 (ttpp) REVERT: A 624 GLN cc_start: 0.7603 (tp-100) cc_final: 0.7288 (tp40) REVERT: A 630 ASP cc_start: 0.7863 (m-30) cc_final: 0.7414 (m-30) REVERT: A 643 TRP cc_start: 0.7725 (t60) cc_final: 0.7296 (t60) REVERT: A 810 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.6019 (mpp) REVERT: A 856 ARG cc_start: 0.7242 (ptp90) cc_final: 0.6866 (ptt180) REVERT: A 863 ILE cc_start: 0.6277 (mm) cc_final: 0.6055 (mm) REVERT: A 866 GLU cc_start: 0.6567 (tm-30) cc_final: 0.6264 (tm-30) REVERT: A 872 GLU cc_start: 0.6716 (mm-30) cc_final: 0.5922 (mm-30) REVERT: A 877 GLN cc_start: 0.7312 (tt0) cc_final: 0.6832 (tt0) REVERT: A 880 LYS cc_start: 0.7461 (tttt) cc_final: 0.7005 (ttpt) REVERT: A 887 ARG cc_start: 0.7658 (mmm-85) cc_final: 0.7306 (mtp85) REVERT: A 911 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6797 (mm-30) REVERT: A 915 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6894 (mt-10) REVERT: A 938 MET cc_start: 0.7951 (tpp) cc_final: 0.7544 (ttm) REVERT: A 946 SER cc_start: 0.8074 (p) cc_final: 0.7289 (t) REVERT: A 960 VAL cc_start: 0.6651 (OUTLIER) cc_final: 0.6386 (p) REVERT: A 966 ASP cc_start: 0.7319 (t0) cc_final: 0.6516 (p0) REVERT: A 986 GLU cc_start: 0.6304 (tt0) cc_final: 0.5335 (tt0) REVERT: A 991 GLU cc_start: 0.8165 (tt0) cc_final: 0.7617 (tp30) REVERT: A 994 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7394 (tm-30) REVERT: A 1059 CYS cc_start: 0.7192 (m) cc_final: 0.6577 (m) REVERT: A 1085 SER cc_start: 0.8328 (t) cc_final: 0.7905 (p) REVERT: A 1105 GLU cc_start: 0.8194 (tt0) cc_final: 0.7343 (pp20) REVERT: A 1122 GLU cc_start: 0.7758 (tp30) cc_final: 0.7429 (mm-30) REVERT: A 1144 ASP cc_start: 0.6789 (m-30) cc_final: 0.6416 (m-30) REVERT: A 1145 VAL cc_start: 0.7944 (t) cc_final: 0.7678 (p) REVERT: A 1190 ARG cc_start: 0.6941 (mmt180) cc_final: 0.6491 (mmm-85) outliers start: 31 outliers final: 24 residues processed: 249 average time/residue: 0.2210 time to fit residues: 72.8376 Evaluate side-chains 263 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 237 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN A 832 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8267 Z= 0.238 Angle : 0.569 8.802 11218 Z= 0.292 Chirality : 0.040 0.152 1348 Planarity : 0.004 0.045 1378 Dihedral : 8.247 146.013 1104 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.52 % Allowed : 20.34 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.27), residues: 1012 helix: 1.89 (0.19), residues: 717 sheet: -0.62 (0.75), residues: 54 loop : -0.24 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 595 HIS 0.004 0.001 HIS A1120 PHE 0.014 0.001 PHE A 625 TYR 0.017 0.001 TYR A 267 ARG 0.005 0.000 ARG A 812 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 240 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.6929 (mm) cc_final: 0.6628 (mt) REVERT: A 149 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6425 (tm-30) REVERT: A 155 ASP cc_start: 0.6153 (t0) cc_final: 0.5546 (t70) REVERT: A 157 HIS cc_start: 0.6790 (m90) cc_final: 0.6405 (m90) REVERT: A 160 MET cc_start: 0.7506 (mmt) cc_final: 0.7271 (mmt) REVERT: A 164 SER cc_start: 0.7523 (m) cc_final: 0.7259 (p) REVERT: A 168 ILE cc_start: 0.6740 (tt) cc_final: 0.6359 (pt) REVERT: A 199 MET cc_start: 0.7239 (mmm) cc_final: 0.6599 (tpp) REVERT: A 209 ASP cc_start: 0.7332 (t0) cc_final: 0.6928 (t0) REVERT: A 219 ASP cc_start: 0.7415 (t0) cc_final: 0.7170 (t0) REVERT: A 238 ASP cc_start: 0.6248 (m-30) cc_final: 0.5929 (m-30) REVERT: A 383 MET cc_start: 0.7412 (mmm) cc_final: 0.7180 (tpp) REVERT: A 424 ILE cc_start: 0.6725 (mm) cc_final: 0.6497 (tp) REVERT: A 443 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6953 (tm-30) REVERT: A 475 GLN cc_start: 0.7370 (tp40) cc_final: 0.6894 (tp-100) REVERT: A 485 ASP cc_start: 0.7902 (m-30) cc_final: 0.7463 (p0) REVERT: A 500 ARG cc_start: 0.7496 (tpp80) cc_final: 0.7192 (tpp80) REVERT: A 573 ARG cc_start: 0.7009 (tpp80) cc_final: 0.6634 (tpp80) REVERT: A 583 ARG cc_start: 0.7890 (tmm160) cc_final: 0.7384 (ttp80) REVERT: A 588 LYS cc_start: 0.7550 (ttpp) cc_final: 0.7164 (ttpp) REVERT: A 602 MET cc_start: 0.7336 (mmm) cc_final: 0.7057 (tpp) REVERT: A 624 GLN cc_start: 0.7602 (tp-100) cc_final: 0.7231 (tp40) REVERT: A 630 ASP cc_start: 0.7864 (m-30) cc_final: 0.7412 (m-30) REVERT: A 633 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8084 (mtmm) REVERT: A 643 TRP cc_start: 0.7730 (t60) cc_final: 0.7326 (t60) REVERT: A 810 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6075 (mpp) REVERT: A 856 ARG cc_start: 0.7249 (ptp90) cc_final: 0.6854 (ptt180) REVERT: A 863 ILE cc_start: 0.6332 (mm) cc_final: 0.6114 (mm) REVERT: A 866 GLU cc_start: 0.6570 (tm-30) cc_final: 0.6279 (tm-30) REVERT: A 872 GLU cc_start: 0.6751 (mm-30) cc_final: 0.5936 (mm-30) REVERT: A 877 GLN cc_start: 0.7316 (tt0) cc_final: 0.6826 (tt0) REVERT: A 880 LYS cc_start: 0.7426 (tttt) cc_final: 0.6975 (ttpt) REVERT: A 887 ARG cc_start: 0.7651 (mmm-85) cc_final: 0.7299 (mtp85) REVERT: A 911 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6802 (mm-30) REVERT: A 915 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6897 (mt-10) REVERT: A 938 MET cc_start: 0.7949 (tpp) cc_final: 0.7558 (ttm) REVERT: A 946 SER cc_start: 0.8060 (p) cc_final: 0.7260 (t) REVERT: A 960 VAL cc_start: 0.6642 (OUTLIER) cc_final: 0.6384 (p) REVERT: A 966 ASP cc_start: 0.7289 (t0) cc_final: 0.6515 (p0) REVERT: A 986 GLU cc_start: 0.6360 (tt0) cc_final: 0.5408 (tt0) REVERT: A 991 GLU cc_start: 0.8155 (tt0) cc_final: 0.7595 (tp30) REVERT: A 994 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7422 (tm-30) REVERT: A 1059 CYS cc_start: 0.7100 (m) cc_final: 0.6532 (m) REVERT: A 1085 SER cc_start: 0.8329 (t) cc_final: 0.7920 (p) REVERT: A 1105 GLU cc_start: 0.8112 (tt0) cc_final: 0.7196 (pp20) REVERT: A 1122 GLU cc_start: 0.7747 (tp30) cc_final: 0.7388 (mm-30) REVERT: A 1144 ASP cc_start: 0.6778 (m-30) cc_final: 0.6299 (m-30) REVERT: A 1145 VAL cc_start: 0.7937 (t) cc_final: 0.7677 (p) REVERT: A 1189 VAL cc_start: 0.6606 (OUTLIER) cc_final: 0.6124 (p) REVERT: A 1190 ARG cc_start: 0.6961 (mmt180) cc_final: 0.6509 (mmm-85) outliers start: 31 outliers final: 23 residues processed: 252 average time/residue: 0.2254 time to fit residues: 75.5551 Evaluate side-chains 266 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 240 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.3980 chunk 93 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8267 Z= 0.209 Angle : 0.565 8.902 11218 Z= 0.288 Chirality : 0.039 0.151 1348 Planarity : 0.004 0.045 1378 Dihedral : 8.250 146.933 1104 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.61 % Allowed : 21.70 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.27), residues: 1012 helix: 1.99 (0.20), residues: 717 sheet: -0.51 (0.75), residues: 55 loop : -0.28 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 595 HIS 0.003 0.001 HIS A1120 PHE 0.013 0.001 PHE A 598 TYR 0.024 0.001 TYR A 267 ARG 0.005 0.000 ARG A 812 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 237 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.6930 (mm) cc_final: 0.6632 (mt) REVERT: A 149 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6505 (tm-30) REVERT: A 155 ASP cc_start: 0.6139 (t0) cc_final: 0.5532 (t70) REVERT: A 157 HIS cc_start: 0.6778 (m90) cc_final: 0.6396 (m90) REVERT: A 160 MET cc_start: 0.7540 (mmt) cc_final: 0.7289 (mmt) REVERT: A 199 MET cc_start: 0.7271 (mmm) cc_final: 0.6655 (tpp) REVERT: A 209 ASP cc_start: 0.7285 (t0) cc_final: 0.6908 (t0) REVERT: A 219 ASP cc_start: 0.7396 (t0) cc_final: 0.7135 (t0) REVERT: A 238 ASP cc_start: 0.6247 (m-30) cc_final: 0.5903 (m-30) REVERT: A 383 MET cc_start: 0.7419 (mmm) cc_final: 0.7189 (tpp) REVERT: A 424 ILE cc_start: 0.6688 (mm) cc_final: 0.6443 (tp) REVERT: A 443 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6923 (tm-30) REVERT: A 475 GLN cc_start: 0.7375 (tp40) cc_final: 0.6904 (tp-100) REVERT: A 485 ASP cc_start: 0.7920 (m-30) cc_final: 0.7444 (p0) REVERT: A 500 ARG cc_start: 0.7496 (tpp80) cc_final: 0.7198 (tpp80) REVERT: A 573 ARG cc_start: 0.7052 (tpp80) cc_final: 0.6719 (tpp80) REVERT: A 579 MET cc_start: 0.7132 (tmm) cc_final: 0.6560 (tmm) REVERT: A 580 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7457 (mm-30) REVERT: A 583 ARG cc_start: 0.7886 (tmm160) cc_final: 0.7358 (ttt-90) REVERT: A 588 LYS cc_start: 0.7563 (ttpp) cc_final: 0.7199 (ttpp) REVERT: A 602 MET cc_start: 0.7208 (mmm) cc_final: 0.6989 (tpp) REVERT: A 612 VAL cc_start: 0.7885 (t) cc_final: 0.7681 (t) REVERT: A 616 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7280 (mt-10) REVERT: A 624 GLN cc_start: 0.7596 (tp-100) cc_final: 0.6654 (tm-30) REVERT: A 630 ASP cc_start: 0.7840 (m-30) cc_final: 0.7371 (m-30) REVERT: A 633 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8063 (mtmm) REVERT: A 643 TRP cc_start: 0.7718 (t60) cc_final: 0.7306 (t60) REVERT: A 810 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.6019 (mpp) REVERT: A 847 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6872 (mm-30) REVERT: A 856 ARG cc_start: 0.7275 (ptp90) cc_final: 0.6845 (ptt180) REVERT: A 863 ILE cc_start: 0.6311 (mm) cc_final: 0.5975 (mm) REVERT: A 866 GLU cc_start: 0.6575 (tm-30) cc_final: 0.6258 (tm-30) REVERT: A 880 LYS cc_start: 0.7455 (tttt) cc_final: 0.7069 (ttpt) REVERT: A 887 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7287 (mtp85) REVERT: A 911 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6792 (mm-30) REVERT: A 915 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6893 (mt-10) REVERT: A 938 MET cc_start: 0.7939 (tpp) cc_final: 0.7542 (ttm) REVERT: A 946 SER cc_start: 0.8058 (p) cc_final: 0.7233 (t) REVERT: A 966 ASP cc_start: 0.7319 (t0) cc_final: 0.6533 (p0) REVERT: A 986 GLU cc_start: 0.6339 (tt0) cc_final: 0.5668 (tt0) REVERT: A 991 GLU cc_start: 0.8147 (tt0) cc_final: 0.7446 (tp30) REVERT: A 994 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7440 (tm-30) REVERT: A 1071 GLU cc_start: 0.7921 (mp0) cc_final: 0.7716 (mp0) REVERT: A 1085 SER cc_start: 0.8306 (t) cc_final: 0.7895 (p) REVERT: A 1105 GLU cc_start: 0.8070 (tt0) cc_final: 0.7304 (pp20) REVERT: A 1122 GLU cc_start: 0.7733 (tp30) cc_final: 0.7374 (mm-30) REVERT: A 1144 ASP cc_start: 0.6734 (m-30) cc_final: 0.6249 (m-30) REVERT: A 1145 VAL cc_start: 0.7934 (t) cc_final: 0.7682 (p) REVERT: A 1189 VAL cc_start: 0.6653 (OUTLIER) cc_final: 0.6155 (p) REVERT: A 1190 ARG cc_start: 0.6991 (mmt180) cc_final: 0.6638 (mmm-85) outliers start: 23 outliers final: 21 residues processed: 246 average time/residue: 0.2348 time to fit residues: 76.0327 Evaluate side-chains 257 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 234 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.5980 chunk 81 optimal weight: 0.0270 chunk 33 optimal weight: 0.0370 chunk 83 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112549 restraints weight = 12802.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115738 restraints weight = 5902.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117741 restraints weight = 3437.782| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8267 Z= 0.174 Angle : 0.567 9.030 11218 Z= 0.287 Chirality : 0.038 0.153 1348 Planarity : 0.004 0.045 1378 Dihedral : 8.241 147.439 1104 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.84 % Allowed : 22.05 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.27), residues: 1012 helix: 2.14 (0.20), residues: 712 sheet: -0.39 (0.77), residues: 55 loop : -0.23 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 595 HIS 0.002 0.000 HIS A 157 PHE 0.013 0.001 PHE A1067 TYR 0.028 0.001 TYR A 743 ARG 0.008 0.000 ARG A 812 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2164.24 seconds wall clock time: 39 minutes 6.68 seconds (2346.68 seconds total)