Starting phenix.real_space_refine on Thu Sep 18 05:29:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9klo_62411/09_2025/9klo_62411.cif Found real_map, /net/cci-nas-00/data/ceres_data/9klo_62411/09_2025/9klo_62411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9klo_62411/09_2025/9klo_62411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9klo_62411/09_2025/9klo_62411.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9klo_62411/09_2025/9klo_62411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9klo_62411/09_2025/9klo_62411.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 165 5.49 5 S 36 5.16 5 C 8449 2.51 5 N 2612 2.21 5 O 3106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14372 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1396, 10852 Classifications: {'peptide': 1396} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 58, 'TRANS': 1337} Chain breaks: 9 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 16, 'GLN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 133 Chain: "B" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2201 Inner-chain residues flagged as termini: ['pdbres=" C B 82 "'] Classifications: {'RNA': 103} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 47, 'rna3p_pyr': 40} Link IDs: {'rna2p': 16, 'rna3p': 86} Chain: "C" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 690 Classifications: {'DNA': 34} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 621 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.65, per 1000 atoms: 0.25 Number of scatterers: 14372 At special positions: 0 Unit cell: (110.285, 120.834, 131.383, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 36 16.00 P 165 15.00 O 3106 8.00 N 2612 7.00 C 8449 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 533.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2610 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 8 sheets defined 55.8% alpha, 9.0% beta 49 base pairs and 99 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 24 through 52 removed outlier: 3.598A pdb=" N ALA A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 54 No H-bonds generated for 'chain 'A' and resid 53 through 54' Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.514A pdb=" N ALA A 59 " --> pdb=" O HIS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 106 through 125 Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 176 through 185 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.534A pdb=" N LYS A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 removed outlier: 3.720A pdb=" N MET A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 269 Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.848A pdb=" N VAL A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.903A pdb=" N ASN A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 330 Processing helix chain 'A' and resid 337 through 352 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.661A pdb=" N THR A 369 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER A 370 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 418 removed outlier: 3.712A pdb=" N PHE A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 removed outlier: 3.559A pdb=" N LEU A 424 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.916A pdb=" N GLU A 458 " --> pdb=" O LYS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 474 through 486 Processing helix chain 'A' and resid 496 through 503 removed outlier: 3.670A pdb=" N PHE A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 512 removed outlier: 6.295A pdb=" N GLU A 507 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS A 510 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.510A pdb=" N GLY A 516 " --> pdb=" O HIS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 543 removed outlier: 3.972A pdb=" N ILE A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.537A pdb=" N ARG A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 641 through 648 removed outlier: 3.732A pdb=" N ALA A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 691 through 704 removed outlier: 3.611A pdb=" N ASP A 704 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 729 removed outlier: 3.889A pdb=" N SER A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.549A pdb=" N LYS A 745 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 746 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 747 " --> pdb=" O ASN A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 747' Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'A' and resid 868 through 882 Processing helix chain 'A' and resid 887 through 895 removed outlier: 3.642A pdb=" N ALA A 895 " --> pdb=" O ARG A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 914 Processing helix chain 'A' and resid 936 through 966 removed outlier: 4.173A pdb=" N LYS A 953 " --> pdb=" O ARG A 949 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 958 " --> pdb=" O TYR A 954 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 959 " --> pdb=" O HIS A 955 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 removed outlier: 3.658A pdb=" N SER A 988 " --> pdb=" O ASP A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1015 Processing helix chain 'A' and resid 1021 through 1029 Processing helix chain 'A' and resid 1054 through 1073 Proline residue: A1066 - end of helix removed outlier: 3.773A pdb=" N ALA A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1108 removed outlier: 3.768A pdb=" N LYS A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A1106 " --> pdb=" O TRP A1102 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE A1107 " --> pdb=" O MET A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1115 Processing helix chain 'A' and resid 1116 through 1120 removed outlier: 3.925A pdb=" N ILE A1119 " --> pdb=" O THR A1116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A1120 " --> pdb=" O PRO A1117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1116 through 1120' Processing helix chain 'A' and resid 1126 through 1140 removed outlier: 3.544A pdb=" N LEU A1130 " --> pdb=" O SER A1126 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1140 " --> pdb=" O PHE A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'A' and resid 1162 through 1190 removed outlier: 3.570A pdb=" N LEU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1240 Processing helix chain 'A' and resid 1243 through 1258 Processing helix chain 'A' and resid 1269 through 1273 removed outlier: 3.638A pdb=" N ARG A1272 " --> pdb=" O TYR A1269 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN A1273 " --> pdb=" O THR A1270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1269 through 1273' Processing helix chain 'A' and resid 1295 through 1309 Processing helix chain 'A' and resid 1311 through 1325 Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.786A pdb=" N LYS A1359 " --> pdb=" O PRO A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1375 removed outlier: 3.923A pdb=" N ALA A1375 " --> pdb=" O ILE A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1481 removed outlier: 3.501A pdb=" N TYR A1461 " --> pdb=" O ASP A1457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 561 through 562 removed outlier: 3.687A pdb=" N GLY A 669 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 90 removed outlier: 3.949A pdb=" N ALA A 101 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN A 155 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 99 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 357 removed outlier: 4.238A pdb=" N LEU A 356 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 635 through 637 Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 812 removed outlier: 3.626A pdb=" N ARG A 810 " --> pdb=" O GLU A 825 " (cutoff:3.500A) removed outlier: 21.689A pdb=" N GLU A 824 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 17.230A pdb=" N PHE A 854 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 13.411A pdb=" N SER A 826 " --> pdb=" O ARG A 852 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ARG A 852 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL A 828 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 778 " --> pdb=" O ASP A 851 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN A 853 " --> pdb=" O CYS A 776 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N CYS A 776 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU A 855 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA A 774 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A 764 " --> pdb=" O ILE A1218 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU A1220 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N VAL A 766 " --> pdb=" O GLU A1220 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A1217 " --> pdb=" O ARG A1263 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL A1265 " --> pdb=" O VAL A1217 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A1219 " --> pdb=" O VAL A1265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 969 through 972 Processing sheet with id=AA7, first strand: chain 'A' and resid 1338 through 1341 Processing sheet with id=AA8, first strand: chain 'A' and resid 1387 through 1391 570 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 128 hydrogen bonds 252 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 99 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2688 1.33 - 1.45: 4387 1.45 - 1.57: 7540 1.57 - 1.68: 328 1.68 - 1.80: 56 Bond restraints: 14999 Sorted by residual: bond pdb=" N TRP A1242 " pdb=" CA TRP A1242 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.33e-02 5.65e+03 7.20e+00 bond pdb=" P DG D 11 " pdb=" OP2 DG D 11 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" O5' C B 115 " pdb=" C5' C B 115 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.66e+00 bond pdb=" P DC C 16 " pdb=" OP1 DC C 16 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.37e+00 bond pdb=" P DC C 16 " pdb=" OP2 DC C 16 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.08e+00 ... (remaining 14994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 20868 2.60 - 5.19: 168 5.19 - 7.79: 21 7.79 - 10.38: 4 10.38 - 12.98: 2 Bond angle restraints: 21063 Sorted by residual: angle pdb=" O3' DG D 11 " pdb=" P DT D 12 " pdb=" O5' DT D 12 " ideal model delta sigma weight residual 104.00 91.02 12.98 1.50e+00 4.44e-01 7.48e+01 angle pdb=" O4' G B 92 " pdb=" C1' G B 92 " pdb=" N9 G B 92 " ideal model delta sigma weight residual 108.20 115.77 -7.57 1.50e+00 4.44e-01 2.55e+01 angle pdb=" O3' DC C 16 " pdb=" P DA C 17 " pdb=" O5' DA C 17 " ideal model delta sigma weight residual 104.00 110.38 -6.38 1.50e+00 4.44e-01 1.81e+01 angle pdb=" C3' DC C 16 " pdb=" O3' DC C 16 " pdb=" P DA C 17 " ideal model delta sigma weight residual 120.20 125.73 -5.53 1.50e+00 4.44e-01 1.36e+01 angle pdb=" O3' C B 59 " pdb=" C3' C B 59 " pdb=" C2' C B 59 " ideal model delta sigma weight residual 113.70 118.66 -4.96 1.50e+00 4.44e-01 1.09e+01 ... (remaining 21058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 8395 35.30 - 70.59: 515 70.59 - 105.89: 42 105.89 - 141.19: 3 141.19 - 176.48: 2 Dihedral angle restraints: 8957 sinusoidal: 4929 harmonic: 4028 Sorted by residual: dihedral pdb=" CA THR A 380 " pdb=" C THR A 380 " pdb=" N ALA A 381 " pdb=" CA ALA A 381 " ideal model delta harmonic sigma weight residual -180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA GLN A1362 " pdb=" C GLN A1362 " pdb=" N ALA A1363 " pdb=" CA ALA A1363 " ideal model delta harmonic sigma weight residual 180.00 -157.55 -22.45 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" C4' DT D 30 " pdb=" C3' DT D 30 " pdb=" O3' DT D 30 " pdb=" P DT D 31 " ideal model delta sinusoidal sigma weight residual 220.00 43.52 176.48 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2354 0.117 - 0.234: 30 0.234 - 0.352: 0 0.352 - 0.469: 4 0.469 - 0.586: 3 Chirality restraints: 2391 Sorted by residual: chirality pdb=" P DC C 16 " pdb=" OP1 DC C 16 " pdb=" OP2 DC C 16 " pdb=" O5' DC C 16 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.59e+00 chirality pdb=" P DG D 11 " pdb=" OP1 DG D 11 " pdb=" OP2 DG D 11 " pdb=" O5' DG D 11 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.56 2.00e-01 2.50e+01 7.96e+00 chirality pdb=" P DT C 15 " pdb=" OP1 DT C 15 " pdb=" OP2 DT C 15 " pdb=" O5' DT C 15 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.52e+00 ... (remaining 2388 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 92 " -0.049 2.00e-02 2.50e+03 2.25e-02 1.51e+01 pdb=" N9 G B 92 " 0.058 2.00e-02 2.50e+03 pdb=" C8 G B 92 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B 92 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G B 92 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G B 92 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G B 92 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G B 92 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G B 92 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G B 92 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 92 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G B 92 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 32 " 0.029 2.00e-02 2.50e+03 1.27e-02 4.81e+00 pdb=" N9 G B 32 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G B 32 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G B 32 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 32 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G B 32 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G B 32 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G B 32 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B 32 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 32 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G B 32 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B 32 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 99 " 0.022 2.00e-02 2.50e+03 1.19e-02 3.17e+00 pdb=" N1 U B 99 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U B 99 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U B 99 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U B 99 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U B 99 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U B 99 " 0.006 2.00e-02 2.50e+03 pdb=" C5 U B 99 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U B 99 " -0.003 2.00e-02 2.50e+03 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 367 2.68 - 3.23: 12347 3.23 - 3.79: 22880 3.79 - 4.34: 30775 4.34 - 4.90: 48479 Nonbonded interactions: 114848 Sorted by model distance: nonbonded pdb=" OD1 ASN A 345 " pdb=" NZ LYS A 349 " model vdw 2.122 3.120 nonbonded pdb=" NH1 ARG A 762 " pdb=" OE2 GLU A 780 " model vdw 2.161 3.120 nonbonded pdb=" OG1 THR A 295 " pdb=" OD2 ASP A 323 " model vdw 2.166 3.040 nonbonded pdb=" OG SER A 276 " pdb=" OD1 ASN A 278 " model vdw 2.173 3.040 nonbonded pdb="CA CA A1501 " pdb=" O HOH A1602 " model vdw 2.191 2.510 ... (remaining 114843 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.006 0.044 14999 Z= 0.285 Angle : 0.668 12.977 21063 Z= 0.361 Chirality : 0.049 0.586 2391 Planarity : 0.005 0.041 2112 Dihedral : 19.584 176.484 6347 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.19 % Allowed : 0.65 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.23), residues: 1376 helix: 2.12 (0.20), residues: 687 sheet: -0.18 (0.41), residues: 149 loop : -0.83 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1101 TYR 0.012 0.002 TYR A 978 PHE 0.029 0.002 PHE A1292 TRP 0.014 0.002 TRP A1102 HIS 0.011 0.001 HIS A 770 Details of bonding type rmsd covalent geometry : bond 0.00638 (14999) covalent geometry : angle 0.66811 (21063) hydrogen bonds : bond 0.14039 ( 698) hydrogen bonds : angle 4.86661 ( 1872) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8360 (t0) cc_final: 0.8124 (t0) REVERT: A 301 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7679 (tp30) REVERT: A 521 SER cc_start: 0.9045 (m) cc_final: 0.8752 (t) REVERT: A 750 GLN cc_start: 0.8310 (mp10) cc_final: 0.7850 (mm-40) REVERT: A 975 ASP cc_start: 0.8756 (t0) cc_final: 0.8466 (t0) REVERT: A 1017 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7505 (mtm-85) REVERT: A 1020 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.6998 (mtt-85) REVERT: A 1039 GLN cc_start: 0.7573 (mt0) cc_final: 0.7231 (mt0) REVERT: A 1159 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8198 (mp0) REVERT: A 1196 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7553 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8157 (tt0) cc_final: 0.7887 (tt0) REVERT: A 1346 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8536 (mm-30) REVERT: A 1364 ASP cc_start: 0.8504 (m-30) cc_final: 0.8254 (m-30) outliers start: 2 outliers final: 0 residues processed: 126 average time/residue: 0.9059 time to fit residues: 122.0232 Evaluate side-chains 69 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1346 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0070 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS A1440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.083164 restraints weight = 23723.530| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.25 r_work: 0.2900 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14999 Z= 0.136 Angle : 0.515 10.117 21063 Z= 0.280 Chirality : 0.035 0.323 2391 Planarity : 0.004 0.048 2112 Dihedral : 20.533 179.910 3806 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.20 % Allowed : 7.41 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.23), residues: 1376 helix: 2.57 (0.20), residues: 685 sheet: -0.03 (0.42), residues: 149 loop : -0.69 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1101 TYR 0.013 0.001 TYR A 291 PHE 0.012 0.001 PHE A 43 TRP 0.017 0.001 TRP A1102 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00284 (14999) covalent geometry : angle 0.51505 (21063) hydrogen bonds : bond 0.04724 ( 698) hydrogen bonds : angle 3.56999 ( 1872) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8459 (t0) cc_final: 0.8105 (t0) REVERT: A 301 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7459 (tp30) REVERT: A 453 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8004 (mtt-85) REVERT: A 521 SER cc_start: 0.9004 (m) cc_final: 0.8659 (t) REVERT: A 719 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6585 (mp10) REVERT: A 750 GLN cc_start: 0.8438 (mp10) cc_final: 0.7996 (mm-40) REVERT: A 975 ASP cc_start: 0.8780 (t0) cc_final: 0.8461 (t0) REVERT: A 1017 ARG cc_start: 0.7671 (mtp180) cc_final: 0.7140 (mtm-85) REVERT: A 1020 ARG cc_start: 0.7802 (mmm-85) cc_final: 0.7534 (mtt-85) REVERT: A 1103 MET cc_start: 0.8684 (tpt) cc_final: 0.8321 (tpp) REVERT: A 1159 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7969 (mp0) REVERT: A 1196 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7432 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8447 (tt0) cc_final: 0.7962 (tt0) REVERT: A 1286 ASP cc_start: 0.8525 (m-30) cc_final: 0.8298 (m-30) outliers start: 13 outliers final: 1 residues processed: 93 average time/residue: 0.8449 time to fit residues: 84.5747 Evaluate side-chains 76 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1304 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 121 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 28 optimal weight: 0.0570 chunk 0 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.114416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.083661 restraints weight = 23833.564| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.24 r_work: 0.2889 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14999 Z= 0.168 Angle : 0.527 10.403 21063 Z= 0.285 Chirality : 0.036 0.343 2391 Planarity : 0.004 0.042 2112 Dihedral : 20.487 178.955 3803 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.48 % Allowed : 10.01 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.23), residues: 1376 helix: 2.66 (0.20), residues: 693 sheet: 0.02 (0.42), residues: 147 loop : -0.61 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1101 TYR 0.022 0.002 TYR A1038 PHE 0.016 0.001 PHE A1292 TRP 0.018 0.001 TRP A 177 HIS 0.003 0.001 HIS A 666 Details of bonding type rmsd covalent geometry : bond 0.00373 (14999) covalent geometry : angle 0.52685 (21063) hydrogen bonds : bond 0.05272 ( 698) hydrogen bonds : angle 3.51732 ( 1872) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8426 (t0) cc_final: 0.8026 (t0) REVERT: A 254 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6513 (mp0) REVERT: A 301 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7496 (tp30) REVERT: A 362 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7565 (ttt90) REVERT: A 521 SER cc_start: 0.9012 (m) cc_final: 0.8659 (t) REVERT: A 719 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.6864 (mp10) REVERT: A 750 GLN cc_start: 0.8631 (mp10) cc_final: 0.8099 (mm-40) REVERT: A 975 ASP cc_start: 0.8821 (t0) cc_final: 0.8504 (t0) REVERT: A 1017 ARG cc_start: 0.7738 (mtp180) cc_final: 0.7334 (mtm-85) REVERT: A 1103 MET cc_start: 0.8936 (tpt) cc_final: 0.8580 (tpp) REVERT: A 1159 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8183 (mp0) REVERT: A 1196 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7600 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8630 (tt0) cc_final: 0.8045 (tt0) REVERT: A 1240 MET cc_start: 0.8819 (ptm) cc_final: 0.8512 (ptm) REVERT: A 1362 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.6906 (tm-30) outliers start: 16 outliers final: 2 residues processed: 80 average time/residue: 0.9522 time to fit residues: 81.7129 Evaluate side-chains 73 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 47 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 152 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 131 optimal weight: 0.0040 overall best weight: 1.2396 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.115513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.084874 restraints weight = 23778.301| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.24 r_work: 0.2913 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14999 Z= 0.139 Angle : 0.492 10.173 21063 Z= 0.267 Chirality : 0.035 0.326 2391 Planarity : 0.004 0.040 2112 Dihedral : 20.351 178.046 3803 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.67 % Allowed : 10.84 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.23), residues: 1376 helix: 2.88 (0.20), residues: 687 sheet: 0.07 (0.42), residues: 149 loop : -0.52 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1392 TYR 0.015 0.001 TYR A1038 PHE 0.011 0.001 PHE A1292 TRP 0.016 0.001 TRP A 177 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00301 (14999) covalent geometry : angle 0.49234 (21063) hydrogen bonds : bond 0.04620 ( 698) hydrogen bonds : angle 3.32415 ( 1872) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8054 (tt0) cc_final: 0.7683 (tm-30) REVERT: A 172 THR cc_start: 0.8314 (m) cc_final: 0.8060 (p) REVERT: A 301 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7448 (tp30) REVERT: A 362 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7553 (ttt90) REVERT: A 453 ARG cc_start: 0.8399 (mtt90) cc_final: 0.8134 (mtt-85) REVERT: A 679 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8288 (mt-10) REVERT: A 719 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.6799 (mp10) REVERT: A 750 GLN cc_start: 0.8627 (mp10) cc_final: 0.8061 (mm-40) REVERT: A 975 ASP cc_start: 0.8796 (t0) cc_final: 0.8488 (t0) REVERT: A 1017 ARG cc_start: 0.7725 (mtp180) cc_final: 0.7315 (mtm-85) REVERT: A 1103 MET cc_start: 0.8816 (tpt) cc_final: 0.8508 (tpp) REVERT: A 1159 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8177 (mp0) REVERT: A 1196 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7577 (mtt-85) REVERT: A 1229 GLU cc_start: 0.8655 (tt0) cc_final: 0.8055 (tt0) REVERT: A 1240 MET cc_start: 0.8709 (ptm) cc_final: 0.8392 (ptm) REVERT: A 1362 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: A 1392 ARG cc_start: 0.8530 (tpp80) cc_final: 0.8316 (tpp80) outliers start: 18 outliers final: 3 residues processed: 85 average time/residue: 0.9094 time to fit residues: 83.0454 Evaluate side-chains 76 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1174 GLU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.112570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.081637 restraints weight = 23827.372| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.21 r_work: 0.2889 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14999 Z= 0.169 Angle : 0.523 10.262 21063 Z= 0.282 Chirality : 0.036 0.333 2391 Planarity : 0.004 0.041 2112 Dihedral : 20.365 178.912 3803 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.04 % Allowed : 11.31 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.23), residues: 1376 helix: 2.86 (0.20), residues: 688 sheet: 0.03 (0.42), residues: 149 loop : -0.53 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1101 TYR 0.013 0.001 TYR A1038 PHE 0.015 0.001 PHE A1292 TRP 0.017 0.001 TRP A 177 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00376 (14999) covalent geometry : angle 0.52253 (21063) hydrogen bonds : bond 0.05152 ( 698) hydrogen bonds : angle 3.39247 ( 1872) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8040 (tt0) cc_final: 0.7663 (tm-30) REVERT: A 150 ASP cc_start: 0.8396 (t0) cc_final: 0.8081 (t0) REVERT: A 172 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.8046 (p) REVERT: A 254 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6419 (mp0) REVERT: A 301 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7426 (tp30) REVERT: A 362 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7466 (ttt90) REVERT: A 453 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8080 (mtt-85) REVERT: A 679 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: A 719 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.6730 (mp10) REVERT: A 750 GLN cc_start: 0.8562 (mp10) cc_final: 0.8036 (mm-40) REVERT: A 975 ASP cc_start: 0.8797 (t0) cc_final: 0.8493 (t0) REVERT: A 1017 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7399 (mtm-85) REVERT: A 1038 TYR cc_start: 0.7196 (t80) cc_final: 0.6907 (t80) REVERT: A 1103 MET cc_start: 0.8856 (tpt) cc_final: 0.8515 (tpp) REVERT: A 1159 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8116 (mp0) REVERT: A 1196 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7555 (mtt-85) REVERT: A 1240 MET cc_start: 0.8705 (ptm) cc_final: 0.8451 (ptm) REVERT: A 1362 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.6922 (tm-30) outliers start: 22 outliers final: 4 residues processed: 83 average time/residue: 0.8506 time to fit residues: 76.1056 Evaluate side-chains 77 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 149 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.108431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.077343 restraints weight = 23484.741| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.02 r_work: 0.2803 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14999 Z= 0.238 Angle : 0.573 10.328 21063 Z= 0.310 Chirality : 0.039 0.355 2391 Planarity : 0.004 0.042 2112 Dihedral : 20.476 179.558 3803 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.04 % Allowed : 12.05 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.23), residues: 1376 helix: 2.61 (0.20), residues: 693 sheet: -0.06 (0.42), residues: 149 loop : -0.64 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1101 TYR 0.012 0.002 TYR A 422 PHE 0.021 0.001 PHE A1292 TRP 0.017 0.001 TRP A 177 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00540 (14999) covalent geometry : angle 0.57305 (21063) hydrogen bonds : bond 0.06146 ( 698) hydrogen bonds : angle 3.60418 ( 1872) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8001 (tt0) cc_final: 0.7669 (tm-30) REVERT: A 150 ASP cc_start: 0.8513 (t0) cc_final: 0.8137 (t0) REVERT: A 172 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.8025 (p) REVERT: A 254 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: A 301 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7497 (tp30) REVERT: A 362 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7438 (ttt90) REVERT: A 453 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8175 (mtt-85) REVERT: A 697 ARG cc_start: 0.8656 (ttp80) cc_final: 0.8091 (ttp-170) REVERT: A 719 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.6794 (mp10) REVERT: A 750 GLN cc_start: 0.8541 (mp10) cc_final: 0.8012 (mm-40) REVERT: A 975 ASP cc_start: 0.8815 (t0) cc_final: 0.8525 (t0) REVERT: A 1017 ARG cc_start: 0.7874 (mtp180) cc_final: 0.7349 (mtm-85) REVERT: A 1038 TYR cc_start: 0.7333 (t80) cc_final: 0.7082 (t80) REVERT: A 1159 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8142 (mp0) REVERT: A 1196 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7586 (mtt-85) REVERT: A 1240 MET cc_start: 0.8793 (ptm) cc_final: 0.8508 (ptm) REVERT: A 1362 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7118 (tm-30) outliers start: 22 outliers final: 3 residues processed: 85 average time/residue: 0.8877 time to fit residues: 81.4063 Evaluate side-chains 75 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.113997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082611 restraints weight = 23897.882| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.24 r_work: 0.2920 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14999 Z= 0.121 Angle : 0.490 10.071 21063 Z= 0.265 Chirality : 0.034 0.291 2391 Planarity : 0.004 0.042 2112 Dihedral : 20.328 177.137 3803 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.85 % Allowed : 13.07 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.23), residues: 1376 helix: 2.95 (0.20), residues: 687 sheet: 0.08 (0.44), residues: 139 loop : -0.50 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1392 TYR 0.010 0.001 TYR A1038 PHE 0.009 0.001 PHE A1292 TRP 0.017 0.001 TRP A1102 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00254 (14999) covalent geometry : angle 0.48954 (21063) hydrogen bonds : bond 0.04453 ( 698) hydrogen bonds : angle 3.26587 ( 1872) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.492 Fit side-chains REVERT: A 133 GLU cc_start: 0.8037 (tt0) cc_final: 0.7703 (tm-30) REVERT: A 150 ASP cc_start: 0.8434 (t0) cc_final: 0.8063 (t0) REVERT: A 172 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.8055 (p) REVERT: A 301 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7502 (tp30) REVERT: A 362 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7416 (ttt90) REVERT: A 453 ARG cc_start: 0.8344 (mtt90) cc_final: 0.8085 (mtt-85) REVERT: A 535 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8213 (m-30) REVERT: A 697 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8053 (ttp-170) REVERT: A 750 GLN cc_start: 0.8537 (mp10) cc_final: 0.8001 (mm-40) REVERT: A 975 ASP cc_start: 0.8782 (t0) cc_final: 0.8502 (t0) REVERT: A 1017 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7390 (mtm-85) REVERT: A 1103 MET cc_start: 0.8642 (tpp) cc_final: 0.8401 (tpp) REVERT: A 1159 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8127 (mp0) REVERT: A 1196 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7556 (mtt-85) REVERT: A 1240 MET cc_start: 0.8724 (ptm) cc_final: 0.8468 (ptm) REVERT: A 1362 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.6795 (tm-30) outliers start: 20 outliers final: 3 residues processed: 85 average time/residue: 0.8855 time to fit residues: 81.2337 Evaluate side-chains 79 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1304 GLN Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 73 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.109448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.078440 restraints weight = 23381.350| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.02 r_work: 0.2827 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 14999 Z= 0.205 Angle : 0.545 10.257 21063 Z= 0.294 Chirality : 0.037 0.296 2391 Planarity : 0.004 0.059 2112 Dihedral : 20.421 179.153 3803 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.95 % Allowed : 12.70 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.23), residues: 1376 helix: 2.69 (0.20), residues: 694 sheet: 0.03 (0.44), residues: 137 loop : -0.57 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1315 TYR 0.012 0.001 TYR A1038 PHE 0.018 0.001 PHE A1292 TRP 0.018 0.001 TRP A 177 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00461 (14999) covalent geometry : angle 0.54536 (21063) hydrogen bonds : bond 0.05619 ( 698) hydrogen bonds : angle 3.47391 ( 1872) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.522 Fit side-chains REVERT: A 133 GLU cc_start: 0.7969 (tt0) cc_final: 0.7651 (tm-30) REVERT: A 150 ASP cc_start: 0.8493 (t0) cc_final: 0.8084 (t0) REVERT: A 172 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8039 (p) REVERT: A 301 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7499 (tp30) REVERT: A 362 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7406 (ttt90) REVERT: A 453 ARG cc_start: 0.8341 (mtt90) cc_final: 0.8087 (mtt-85) REVERT: A 697 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8031 (ttp-170) REVERT: A 750 GLN cc_start: 0.8568 (mp10) cc_final: 0.8046 (mm-40) REVERT: A 780 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8046 (tt0) REVERT: A 975 ASP cc_start: 0.8818 (t0) cc_final: 0.8544 (t0) REVERT: A 1017 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7328 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8084 (mp0) REVERT: A 1196 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7576 (mtt-85) REVERT: A 1240 MET cc_start: 0.8749 (ptm) cc_final: 0.8517 (ptm) REVERT: A 1362 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.6989 (tm-30) outliers start: 21 outliers final: 4 residues processed: 79 average time/residue: 0.9000 time to fit residues: 76.3959 Evaluate side-chains 74 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 145 optimal weight: 10.9990 chunk 103 optimal weight: 0.0970 chunk 139 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.111344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.080267 restraints weight = 23422.958| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.05 r_work: 0.2854 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14999 Z= 0.146 Angle : 0.506 10.069 21063 Z= 0.272 Chirality : 0.035 0.253 2391 Planarity : 0.004 0.044 2112 Dihedral : 20.367 177.699 3803 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.02 % Allowed : 13.81 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.23), residues: 1376 helix: 2.87 (0.20), residues: 687 sheet: 0.03 (0.44), residues: 139 loop : -0.49 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1315 TYR 0.010 0.001 TYR A1038 PHE 0.012 0.001 PHE A1292 TRP 0.017 0.001 TRP A 177 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00318 (14999) covalent geometry : angle 0.50551 (21063) hydrogen bonds : bond 0.04855 ( 698) hydrogen bonds : angle 3.32153 ( 1872) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.488 Fit side-chains REVERT: A 133 GLU cc_start: 0.7953 (tt0) cc_final: 0.7650 (tm-30) REVERT: A 150 ASP cc_start: 0.8470 (t0) cc_final: 0.8047 (t0) REVERT: A 172 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7942 (p) REVERT: A 301 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7517 (tp30) REVERT: A 362 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7341 (ttt90) REVERT: A 453 ARG cc_start: 0.8249 (mtt90) cc_final: 0.7992 (mtt-85) REVERT: A 535 ASP cc_start: 0.8571 (t70) cc_final: 0.8157 (m-30) REVERT: A 697 ARG cc_start: 0.8575 (ttp80) cc_final: 0.7990 (ttp-170) REVERT: A 750 GLN cc_start: 0.8552 (mp10) cc_final: 0.8013 (mm-40) REVERT: A 780 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: A 975 ASP cc_start: 0.8804 (t0) cc_final: 0.8534 (t0) REVERT: A 1017 ARG cc_start: 0.7814 (mtp180) cc_final: 0.7318 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8043 (mp0) REVERT: A 1196 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7544 (mtt-85) REVERT: A 1240 MET cc_start: 0.8682 (ptm) cc_final: 0.8419 (ptm) REVERT: A 1362 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.6823 (tm-30) outliers start: 11 outliers final: 5 residues processed: 79 average time/residue: 0.9264 time to fit residues: 78.5358 Evaluate side-chains 77 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 92 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 103 optimal weight: 0.0470 chunk 136 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 112 optimal weight: 7.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.112797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.081847 restraints weight = 23291.414| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.01 r_work: 0.2885 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14999 Z= 0.126 Angle : 0.487 10.090 21063 Z= 0.261 Chirality : 0.034 0.241 2391 Planarity : 0.004 0.044 2112 Dihedral : 20.272 176.059 3803 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.74 % Allowed : 14.37 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.23), residues: 1376 helix: 2.98 (0.20), residues: 689 sheet: 0.06 (0.44), residues: 139 loop : -0.45 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1315 TYR 0.011 0.001 TYR A1038 PHE 0.009 0.001 PHE A1292 TRP 0.016 0.001 TRP A1102 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00270 (14999) covalent geometry : angle 0.48667 (21063) hydrogen bonds : bond 0.04354 ( 698) hydrogen bonds : angle 3.18859 ( 1872) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7993 (tt0) cc_final: 0.7683 (tm-30) REVERT: A 150 ASP cc_start: 0.8451 (t0) cc_final: 0.8052 (t0) REVERT: A 172 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.8030 (p) REVERT: A 301 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7502 (tp30) REVERT: A 362 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7376 (ttt90) REVERT: A 453 ARG cc_start: 0.8321 (mtt90) cc_final: 0.8064 (mtt-85) REVERT: A 535 ASP cc_start: 0.8581 (t70) cc_final: 0.8175 (m-30) REVERT: A 750 GLN cc_start: 0.8565 (mp10) cc_final: 0.8013 (mm-40) REVERT: A 975 ASP cc_start: 0.8799 (t0) cc_final: 0.8544 (t0) REVERT: A 1017 ARG cc_start: 0.7815 (mtp180) cc_final: 0.7358 (mtm-85) REVERT: A 1159 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8058 (mp0) REVERT: A 1196 ARG cc_start: 0.7983 (mtp85) cc_final: 0.7611 (mtt-85) REVERT: A 1240 MET cc_start: 0.8637 (ptm) cc_final: 0.8338 (ptm) REVERT: A 1362 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.6770 (tm-30) outliers start: 8 outliers final: 4 residues processed: 75 average time/residue: 0.9332 time to fit residues: 75.1650 Evaluate side-chains 72 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1362 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 96 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.110264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.079262 restraints weight = 23358.950| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.02 r_work: 0.2842 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14999 Z= 0.177 Angle : 0.529 10.258 21063 Z= 0.284 Chirality : 0.036 0.257 2391 Planarity : 0.004 0.044 2112 Dihedral : 20.346 178.122 3803 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.11 % Allowed : 14.27 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.23), residues: 1376 helix: 2.88 (0.20), residues: 688 sheet: 0.07 (0.44), residues: 137 loop : -0.50 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1315 TYR 0.013 0.001 TYR A1038 PHE 0.015 0.001 PHE A1292 TRP 0.019 0.001 TRP A 177 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00395 (14999) covalent geometry : angle 0.52881 (21063) hydrogen bonds : bond 0.05261 ( 698) hydrogen bonds : angle 3.38455 ( 1872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4704.41 seconds wall clock time: 80 minutes 53.77 seconds (4853.77 seconds total)