Starting phenix.real_space_refine on Fri Aug 7 10:38:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hlx_52275/08_2026/9hlx_52275.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hlx_52275/08_2026/9hlx_52275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hlx_52275/08_2026/9hlx_52275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hlx_52275/08_2026/9hlx_52275.map" model { file = "/net/cci-nas-00/data/ceres_data/9hlx_52275/08_2026/9hlx_52275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hlx_52275/08_2026/9hlx_52275.cif" } resolution = 3.8 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= 0.007 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 P 41 5.49 5 S 22 5.16 5 C 6372 2.51 5 N 1780 2.21 5 O 2071 1.98 5 H 9966 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20252 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1156, 18950 Classifications: {'peptide': 1156} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 1133} Chain breaks: 1 Chain: "B" Number of atoms: 1302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 1302 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 13, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 18, 'rna3p': 22} Time building chain proxies: 3.39, per 1000 atoms: 0.17 Number of scatterers: 20252 At special positions: 0 Unit cell: (98.28, 108.29, 132.86, 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) S 22 16.00 P 41 15.00 O 2071 8.00 N 1780 7.00 C 6372 6.00 H 9966 1.00 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: 2.16 Conformation dependent library (CDL) restraints added in 619.0 milliseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 9 sheets defined 58.0% alpha, 12.7% beta 5 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 removed outlier: 4.226A pdb=" N ASP A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 54 removed outlier: 3.680A pdb=" N ARG A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 removed outlier: 4.113A pdb=" N LEU A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 93 Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 111 through 136 removed outlier: 3.608A pdb=" N LYS A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 155 Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.552A pdb=" N LEU A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 202 removed outlier: 3.511A pdb=" N GLN A 182 " --> pdb=" O ASN A 178 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 4.223A pdb=" N ILE A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 217 through 222' Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.517A pdb=" N GLU A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 4.323A pdb=" N PHE A 247 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 249 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 292 through 313 Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 332 through 356 Processing helix chain 'A' and resid 358 through 384 Processing helix chain 'A' and resid 384 through 419 removed outlier: 4.098A pdb=" N GLU A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 453 removed outlier: 3.861A pdb=" N SER A 453 " --> pdb=" O GLN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.659A pdb=" N ASN A 485 " --> pdb=" O PHE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 494 removed outlier: 3.512A pdb=" N ASN A 493 " --> pdb=" O LYS A 489 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 498 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 516 through 530 removed outlier: 3.674A pdb=" N LYS A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 537 removed outlier: 3.563A pdb=" N VAL A 536 " --> pdb=" O TYR A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 548 removed outlier: 4.043A pdb=" N ALA A 546 " --> pdb=" O GLN A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 removed outlier: 3.678A pdb=" N PHE A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 587 removed outlier: 3.514A pdb=" N LEU A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.671A pdb=" N ILE A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP A 617 " --> pdb=" O TRP A 613 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 618 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.869A pdb=" N LYS A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 624' Processing helix chain 'A' and resid 685 through 698 Processing helix chain 'A' and resid 699 through 700 No H-bonds generated for 'chain 'A' and resid 699 through 700' Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.545A pdb=" N TYR A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 773 No H-bonds generated for 'chain 'A' and resid 771 through 773' Processing helix chain 'A' and resid 774 through 779 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 790 through 801 Processing helix chain 'A' and resid 828 through 849 Processing helix chain 'A' and resid 869 through 878 Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 887 through 900 Processing helix chain 'A' and resid 908 through 917 removed outlier: 3.687A pdb=" N ARG A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 951 removed outlier: 4.446A pdb=" N PHE A 951 " --> pdb=" O THR A 948 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 948 through 951' Processing helix chain 'A' and resid 968 through 982 removed outlier: 3.624A pdb=" N LYS A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN A 980 " --> pdb=" O ILE A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1024 removed outlier: 4.476A pdb=" N LEU A 995 " --> pdb=" O GLU A 991 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A1000 " --> pdb=" O LYS A 996 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN A1007 " --> pdb=" O ALA A1003 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1047 removed outlier: 3.699A pdb=" N GLU A1044 " --> pdb=" O ASP A1041 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A1046 " --> pdb=" O ILE A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1063 removed outlier: 3.706A pdb=" N ILE A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A1059 " --> pdb=" O GLU A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1066 No H-bonds generated for 'chain 'A' and resid 1064 through 1066' Processing helix chain 'A' and resid 1073 through 1077 removed outlier: 3.615A pdb=" N ALA A1076 " --> pdb=" O SER A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1083 removed outlier: 4.419A pdb=" N GLY A1081 " --> pdb=" O ARG A1078 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A1082 " --> pdb=" O ALA A1079 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A1083 " --> pdb=" O ASN A1080 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1078 through 1083' Processing helix chain 'A' and resid 1135 through 1137 No H-bonds generated for 'chain 'A' and resid 1135 through 1137' Processing helix chain 'A' and resid 1138 through 1156 removed outlier: 3.613A pdb=" N PHE A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A1156 " --> pdb=" O PHE A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1159 No H-bonds generated for 'chain 'A' and resid 1157 through 1159' Processing sheet with id=AA1, first strand: chain 'A' and resid 568 through 573 removed outlier: 3.539A pdb=" N GLU A 468 " --> pdb=" O ARG A 569 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP A 466 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 427 " --> pdb=" O PHE A 465 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE A 467 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ALA A 425 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 13.990A pdb=" N SER A 469 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 16.792A pdb=" N TYR A 423 " --> pdb=" O SER A 469 " (cutoff:3.500A) removed outlier: 13.904A pdb=" N LEU A 421 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 12.508A pdb=" N VAL A 211 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N TYR A 423 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS A 213 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA A 425 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER A 215 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N ILE A 427 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR A 638 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA A 212 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU A 633 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N THR A 669 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 568 through 573 removed outlier: 3.539A pdb=" N GLU A 468 " --> pdb=" O ARG A 569 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP A 466 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 427 " --> pdb=" O PHE A 465 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE A 467 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ALA A 425 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 13.990A pdb=" N SER A 469 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 16.792A pdb=" N TYR A 423 " --> pdb=" O SER A 469 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N HIS A 434 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 593 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE A 590 " --> pdb=" O GLN A 17 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 17 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 13 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 6 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR A 664 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 277 Processing sheet with id=AA5, first strand: chain 'A' and resid 809 through 810 removed outlier: 6.949A pdb=" N GLU A1026 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE A 707 " --> pdb=" O GLU A1026 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A1032 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N GLY A1096 " --> pdb=" O GLY A1027 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A1029 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A1098 " --> pdb=" O ILE A1029 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS A1031 " --> pdb=" O ILE A1098 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 748 through 753 Processing sheet with id=AA7, first strand: chain 'A' and resid 759 through 761 Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 818 Processing sheet with id=AA9, first strand: chain 'A' and resid 933 through 935 482 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5079 1.03 - 1.23: 5089 1.23 - 1.42: 5184 1.42 - 1.62: 5125 1.62 - 1.81: 34 Bond restraints: 20511 Sorted by residual: bond pdb=" C6 A B 33 " pdb=" N6 A B 33 " ideal model delta sigma weight residual 1.335 1.229 0.106 8.00e-03 1.56e+04 1.74e+02 bond pdb=" C6 A B 25 " pdb=" N6 A B 25 " ideal model delta sigma weight residual 1.335 1.230 0.105 8.00e-03 1.56e+04 1.73e+02 bond pdb=" C6 A B 35 " pdb=" N6 A B 35 " ideal model delta sigma weight residual 1.335 1.231 0.104 8.00e-03 1.56e+04 1.70e+02 bond pdb=" C4 C B 51 " pdb=" N4 C B 51 " ideal model delta sigma weight residual 1.335 1.238 0.097 9.00e-03 1.23e+04 1.17e+02 bond pdb=" C4 C B 50 " pdb=" N4 C B 50 " ideal model delta sigma weight residual 1.335 1.238 0.097 9.00e-03 1.23e+04 1.16e+02 ... (remaining 20506 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 27228 2.60 - 5.21: 6439 5.21 - 7.81: 2859 7.81 - 10.41: 487 10.41 - 13.01: 84 Bond angle restraints: 37097 Sorted by residual: angle pdb=" N1 A B 33 " pdb=" C2 A B 33 " pdb=" N3 A B 33 " ideal model delta sigma weight residual 129.30 135.74 -6.44 5.00e-01 4.00e+00 1.66e+02 angle pdb=" N9 A B 33 " pdb=" C8 A B 33 " pdb=" N7 A B 33 " ideal model delta sigma weight residual 113.80 120.17 -6.37 5.00e-01 4.00e+00 1.62e+02 angle pdb=" N1 A B 35 " pdb=" C2 A B 35 " pdb=" N3 A B 35 " ideal model delta sigma weight residual 129.30 135.49 -6.19 5.00e-01 4.00e+00 1.53e+02 angle pdb=" N9 G B 34 " pdb=" C8 G B 34 " pdb=" N7 G B 34 " ideal model delta sigma weight residual 113.10 119.18 -6.08 5.00e-01 4.00e+00 1.48e+02 angle pdb=" N1 A B 25 " pdb=" C2 A B 25 " pdb=" N3 A B 25 " ideal model delta sigma weight residual 129.30 135.28 -5.98 5.00e-01 4.00e+00 1.43e+02 ... (remaining 37092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 9267 35.53 - 71.06: 271 71.06 - 106.59: 48 106.59 - 142.12: 2 142.12 - 177.65: 6 Dihedral angle restraints: 9594 sinusoidal: 5605 harmonic: 3989 Sorted by residual: dihedral pdb=" O4' U B 49 " pdb=" C1' U B 49 " pdb=" N1 U B 49 " pdb=" C2 U B 49 " ideal model delta sinusoidal sigma weight residual 232.00 55.58 176.42 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C B 13 " pdb=" C1' C B 13 " pdb=" N1 C B 13 " pdb=" C2 C B 13 " ideal model delta sinusoidal sigma weight residual 232.00 67.61 164.39 1 1.70e+01 3.46e-03 6.52e+01 dihedral pdb=" O4' U B 43 " pdb=" C1' U B 43 " pdb=" N1 U B 43 " pdb=" C2 U B 43 " ideal model delta sinusoidal sigma weight residual 232.00 68.99 163.01 1 1.70e+01 3.46e-03 6.50e+01 ... (remaining 9591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 933 0.149 - 0.299: 54 0.299 - 0.448: 106 0.448 - 0.597: 407 0.597 - 0.746: 113 Chirality restraints: 1613 Sorted by residual: chirality pdb=" CG LEU A 778 " pdb=" CB LEU A 778 " pdb=" CD1 LEU A 778 " pdb=" CD2 LEU A 778 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CG LEU A 475 " pdb=" CB LEU A 475 " pdb=" CD1 LEU A 475 " pdb=" CD2 LEU A 475 " both_signs ideal model delta sigma weight residual False -2.59 -1.85 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CG LEU A 408 " pdb=" CB LEU A 408 " pdb=" CD1 LEU A 408 " pdb=" CD2 LEU A 408 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.33e+01 ... (remaining 1610 not shown) Planarity restraints: 2862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 26 " -0.304 2.00e-02 2.50e+03 1.22e-01 4.07e+02 pdb=" N1 C B 26 " 0.055 2.00e-02 2.50e+03 pdb=" C2 C B 26 " 0.048 2.00e-02 2.50e+03 pdb=" O2 C B 26 " 0.174 2.00e-02 2.50e+03 pdb=" N3 C B 26 " -0.023 2.00e-02 2.50e+03 pdb=" C4 C B 26 " -0.064 2.00e-02 2.50e+03 pdb=" N4 C B 26 " -0.113 2.00e-02 2.50e+03 pdb=" C5 C B 26 " 0.024 2.00e-02 2.50e+03 pdb=" C6 C B 26 " 0.076 2.00e-02 2.50e+03 pdb=" H5 C B 26 " 0.026 2.00e-02 2.50e+03 pdb=" H6 C B 26 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 37 " 0.254 2.00e-02 2.50e+03 9.94e-02 3.46e+02 pdb=" N9 G B 37 " -0.027 2.00e-02 2.50e+03 pdb=" C8 G B 37 " -0.069 2.00e-02 2.50e+03 pdb=" N7 G B 37 " -0.064 2.00e-02 2.50e+03 pdb=" C5 G B 37 " -0.030 2.00e-02 2.50e+03 pdb=" C6 G B 37 " 0.020 2.00e-02 2.50e+03 pdb=" O6 G B 37 " 0.062 2.00e-02 2.50e+03 pdb=" N1 G B 37 " 0.022 2.00e-02 2.50e+03 pdb=" C2 G B 37 " -0.028 2.00e-02 2.50e+03 pdb=" N2 G B 37 " -0.164 2.00e-02 2.50e+03 pdb=" N3 G B 37 " -0.037 2.00e-02 2.50e+03 pdb=" C4 G B 37 " -0.036 2.00e-02 2.50e+03 pdb=" H8 G B 37 " -0.060 2.00e-02 2.50e+03 pdb=" H1 G B 37 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 27 " 0.172 2.00e-02 2.50e+03 1.03e-01 3.19e+02 pdb=" N1 U B 27 " 0.022 2.00e-02 2.50e+03 pdb=" C2 U B 27 " 0.062 2.00e-02 2.50e+03 pdb=" O2 U B 27 " -0.109 2.00e-02 2.50e+03 pdb=" N3 U B 27 " 0.065 2.00e-02 2.50e+03 pdb=" C4 U B 27 " 0.081 2.00e-02 2.50e+03 pdb=" O4 U B 27 " 0.125 2.00e-02 2.50e+03 pdb=" C5 U B 27 " -0.011 2.00e-02 2.50e+03 pdb=" C6 U B 27 " -0.058 2.00e-02 2.50e+03 pdb=" H5 U B 27 " -0.035 2.00e-02 2.50e+03 pdb=" H3 U B 27 " -0.182 2.00e-02 2.50e+03 pdb=" H6 U B 27 " -0.133 2.00e-02 2.50e+03 ... (remaining 2859 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.08: 421 2.08 - 2.71: 30421 2.71 - 3.34: 55811 3.34 - 3.97: 66249 3.97 - 4.60: 103726 Nonbonded interactions: 256628 Sorted by model distance: nonbonded pdb=" O ARG A 983 " pdb="HH11 ARG A 983 " model vdw 1.444 2.450 nonbonded pdb=" OD2 ASP A 597 " pdb=" HG1 THR A 610 " model vdw 1.544 2.450 nonbonded pdb=" OE1 GLU A 81 " pdb=" H GLU A 81 " model vdw 1.557 2.450 nonbonded pdb=" OE1 GLU A 517 " pdb=" H LEU A 556 " model vdw 1.566 2.450 nonbonded pdb=" HZ3 LYS A1001 " pdb=" O SER A1047 " model vdw 1.566 2.450 ... (remaining 256623 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 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: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.120 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 22.720 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 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 : 0.037 0.146 10545 Z= 2.025 Angle : 2.822 12.660 14364 Z= 1.947 Chirality : 0.344 0.746 1613 Planarity : 0.011 0.139 1702 Dihedral : 17.659 177.645 4306 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.96 % Allowed : 6.07 % Favored : 92.97 % Cbeta Deviations : 22.94 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.24), residues: 1152 helix: 0.33 (0.22), residues: 532 sheet: 1.24 (0.56), residues: 86 loop : -1.17 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 639 TYR 0.088 0.012 TYR A 472 PHE 0.076 0.009 PHE A 935 TRP 0.040 0.006 TRP A 835 HIS 0.011 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.03740 / 2.02 (10545) covalent geometry : angle 2.82219 / 1.95 (14364) hydrogen bonds : bond 0.18757 / 11.46 ( 485) hydrogen bonds : angle 6.25544 / 4.56 ( 1380) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASN cc_start: 0.7901 (t0) cc_final: 0.7525 (m-40) REVERT: A 30 GLN cc_start: 0.8228 (mt0) cc_final: 0.7986 (mt0) REVERT: A 47 ASP cc_start: 0.8417 (t70) cc_final: 0.8051 (t0) REVERT: A 72 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6555 (tm-30) REVERT: A 178 ASN cc_start: 0.7183 (p0) cc_final: 0.6815 (p0) REVERT: A 479 CYS cc_start: 0.8060 (t) cc_final: 0.7711 (m) REVERT: A 545 GLN cc_start: 0.8366 (tp40) cc_final: 0.7993 (tp-100) REVERT: A 627 GLU cc_start: 0.7389 (tp30) cc_final: 0.6673 (tt0) REVERT: A 679 LYS cc_start: 0.6936 (tptm) cc_final: 0.6666 (ttpt) REVERT: A 893 LYS cc_start: 0.8593 (mttt) cc_final: 0.8231 (tttt) REVERT: A 970 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7250 (tp30) REVERT: A 1124 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8184 (mtpp) outliers start: 10 outliers final: 2 residues processed: 192 average time/residue: 0.2505 time to fit residues: 66.3395 Evaluate side-chains 126 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 880 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 788 ASN A 945 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.187770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139237 restraints weight = 41665.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141526 restraints weight = 27945.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.141781 restraints weight = 27418.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.142981 restraints weight = 16442.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.147147 restraints weight = 14722.504| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10545 Z= 0.159 Angle : 0.640 7.216 14364 Z= 0.365 Chirality : 0.042 0.278 1613 Planarity : 0.004 0.044 1702 Dihedral : 18.724 178.743 1871 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.25 % Allowed : 8.67 % Favored : 90.08 % 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 are not related in a simple way. whole: 1.06 (0.25), residues: 1152 helix: 2.07 (0.22), residues: 539 sheet: 0.95 (0.51), residues: 106 loop : -0.90 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 629 TYR 0.022 0.002 TYR A 659 PHE 0.019 0.001 PHE A 939 TRP 0.005 0.001 TRP A 466 HIS 0.006 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (10545) covalent geometry : angle 0.64021 / 0.37 (14364) hydrogen bonds : bond 0.05577 / 3.52 ( 485) hydrogen bonds : angle 5.04390 / 3.67 ( 1380) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8625 (t70) cc_final: 0.8081 (t0) REVERT: A 72 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7344 (tm-30) REVERT: A 178 ASN cc_start: 0.9023 (p0) cc_final: 0.8725 (p0) REVERT: A 387 TRP cc_start: 0.9130 (t-100) cc_final: 0.8852 (t-100) REVERT: A 679 LYS cc_start: 0.8146 (tptm) cc_final: 0.7712 (ttpt) REVERT: A 797 MET cc_start: 0.8536 (tmm) cc_final: 0.8230 (tmm) REVERT: A 845 GLU cc_start: 0.8108 (tp30) cc_final: 0.7858 (tp30) REVERT: A 979 TYR cc_start: 0.6107 (m-80) cc_final: 0.4917 (m-10) REVERT: A 1124 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8174 (mtpp) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 0.2287 time to fit residues: 46.3821 Evaluate side-chains 118 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1109 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.196016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145342 restraints weight = 41517.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.146234 restraints weight = 28083.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148647 restraints weight = 25452.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149630 restraints weight = 17437.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150195 restraints weight = 15979.992| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10545 Z= 0.139 Angle : 0.540 6.181 14364 Z= 0.307 Chirality : 0.039 0.309 1613 Planarity : 0.003 0.042 1702 Dihedral : 18.741 179.667 1866 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.25 % Allowed : 9.92 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.26), residues: 1152 helix: 2.48 (0.23), residues: 538 sheet: 0.64 (0.49), residues: 116 loop : -0.84 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 768 TYR 0.013 0.001 TYR A 659 PHE 0.020 0.001 PHE A 935 TRP 0.009 0.001 TRP A 466 HIS 0.015 0.002 HIS A 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (10545) covalent geometry : angle 0.54021 / 0.31 (14364) hydrogen bonds : bond 0.04834 / 3.04 ( 485) hydrogen bonds : angle 4.66811 / 3.40 ( 1380) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASN cc_start: 0.8296 (t0) cc_final: 0.7896 (t0) REVERT: A 47 ASP cc_start: 0.8555 (t70) cc_final: 0.8017 (t0) REVERT: A 72 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 178 ASN cc_start: 0.9036 (p0) cc_final: 0.8770 (p0) REVERT: A 387 TRP cc_start: 0.9124 (t-100) cc_final: 0.8866 (t-100) REVERT: A 403 LYS cc_start: 0.8840 (tppp) cc_final: 0.8337 (tppp) REVERT: A 791 GLU cc_start: 0.8007 (mp0) cc_final: 0.7791 (tm-30) REVERT: A 797 MET cc_start: 0.8530 (tmm) cc_final: 0.8248 (tmm) REVERT: A 845 GLU cc_start: 0.8004 (tp30) cc_final: 0.7721 (tp30) REVERT: A 979 TYR cc_start: 0.5613 (m-80) cc_final: 0.5085 (m-80) REVERT: A 1124 LYS cc_start: 0.8542 (mmmt) cc_final: 0.8135 (mtpp) outliers start: 13 outliers final: 10 residues processed: 123 average time/residue: 0.2029 time to fit residues: 36.8192 Evaluate side-chains 119 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 113 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 64 optimal weight: 0.0570 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.195164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145093 restraints weight = 41654.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146046 restraints weight = 29681.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.149224 restraints weight = 23835.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149663 restraints weight = 16438.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150225 restraints weight = 15424.005| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10545 Z= 0.141 Angle : 0.510 5.535 14364 Z= 0.290 Chirality : 0.038 0.273 1613 Planarity : 0.003 0.043 1702 Dihedral : 18.737 175.916 1866 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.45 % Allowed : 9.73 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.26), residues: 1152 helix: 2.53 (0.23), residues: 538 sheet: 0.51 (0.49), residues: 116 loop : -0.83 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 768 TYR 0.012 0.001 TYR A 659 PHE 0.014 0.001 PHE A 935 TRP 0.010 0.001 TRP A 466 HIS 0.008 0.001 HIS A 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (10545) covalent geometry : angle 0.50994 / 0.29 (14364) hydrogen bonds : bond 0.04458 / 2.82 ( 485) hydrogen bonds : angle 4.50334 / 3.26 ( 1380) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASN cc_start: 0.8344 (t0) cc_final: 0.8003 (t0) REVERT: A 47 ASP cc_start: 0.8689 (t70) cc_final: 0.8088 (t0) REVERT: A 387 TRP cc_start: 0.9116 (t-100) cc_final: 0.8835 (t-100) REVERT: A 403 LYS cc_start: 0.8875 (tptp) cc_final: 0.8369 (tppp) REVERT: A 797 MET cc_start: 0.8507 (tmm) cc_final: 0.8035 (tmm) REVERT: A 845 GLU cc_start: 0.8061 (tp30) cc_final: 0.7768 (tp30) REVERT: A 1124 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8165 (mtpp) outliers start: 15 outliers final: 11 residues processed: 119 average time/residue: 0.1588 time to fit residues: 27.9641 Evaluate side-chains 113 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 15 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 54 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.186931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140240 restraints weight = 40463.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141206 restraints weight = 28420.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143309 restraints weight = 27897.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144878 restraints weight = 17266.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149064 restraints weight = 15514.044| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10545 Z= 0.139 Angle : 0.492 5.484 14364 Z= 0.278 Chirality : 0.038 0.276 1613 Planarity : 0.003 0.046 1702 Dihedral : 18.724 176.252 1866 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.06 % Allowed : 9.83 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.26), residues: 1152 helix: 2.57 (0.23), residues: 544 sheet: 0.43 (0.50), residues: 116 loop : -0.86 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 71 TYR 0.013 0.001 TYR A 979 PHE 0.012 0.001 PHE A 935 TRP 0.011 0.001 TRP A 466 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (10545) covalent geometry : angle 0.49222 / 0.28 (14364) hydrogen bonds : bond 0.04291 / 2.74 ( 485) hydrogen bonds : angle 4.32289 / 3.12 ( 1380) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 TRP cc_start: 0.9063 (t-100) cc_final: 0.8826 (t-100) REVERT: A 403 LYS cc_start: 0.8907 (tptp) cc_final: 0.8332 (tppp) REVERT: A 797 MET cc_start: 0.8482 (tmm) cc_final: 0.8012 (tmm) REVERT: A 845 GLU cc_start: 0.8066 (tp30) cc_final: 0.7779 (tp30) REVERT: A 1124 LYS cc_start: 0.8538 (mmmt) cc_final: 0.8139 (mtpp) outliers start: 11 outliers final: 10 residues processed: 108 average time/residue: 0.2006 time to fit residues: 30.9306 Evaluate side-chains 107 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 934 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 33 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 104 optimal weight: 0.0070 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 986 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.185658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138622 restraints weight = 40272.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137639 restraints weight = 29503.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141488 restraints weight = 26271.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142132 restraints weight = 16983.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142751 restraints weight = 16404.473| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10545 Z= 0.152 Angle : 0.495 7.073 14364 Z= 0.280 Chirality : 0.038 0.272 1613 Planarity : 0.003 0.045 1702 Dihedral : 18.699 176.419 1866 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.35 % Allowed : 10.02 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.26), residues: 1152 helix: 2.55 (0.23), residues: 545 sheet: 0.35 (0.50), residues: 116 loop : -0.84 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 71 TYR 0.019 0.001 TYR A 326 PHE 0.017 0.001 PHE A 899 TRP 0.011 0.001 TRP A 466 HIS 0.003 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (10545) covalent geometry : angle 0.49543 / 0.28 (14364) hydrogen bonds : bond 0.04286 / 2.75 ( 485) hydrogen bonds : angle 4.26968 / 3.07 ( 1380) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 TRP cc_start: 0.9078 (t-100) cc_final: 0.8826 (t-100) REVERT: A 797 MET cc_start: 0.8480 (tmm) cc_final: 0.8022 (tmm) REVERT: A 845 GLU cc_start: 0.8112 (tp30) cc_final: 0.7855 (tp30) REVERT: A 1124 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8143 (mtpp) outliers start: 14 outliers final: 12 residues processed: 109 average time/residue: 0.1855 time to fit residues: 29.0493 Evaluate side-chains 106 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1089 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 90 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 986 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.184770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.138430 restraints weight = 40526.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139968 restraints weight = 29023.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.142856 restraints weight = 24514.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143397 restraints weight = 15841.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144046 restraints weight = 15272.058| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10545 Z= 0.166 Angle : 0.500 6.013 14364 Z= 0.283 Chirality : 0.038 0.279 1613 Planarity : 0.003 0.048 1702 Dihedral : 18.704 176.863 1866 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.64 % Allowed : 10.02 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.26), residues: 1152 helix: 2.46 (0.23), residues: 546 sheet: 0.26 (0.50), residues: 117 loop : -0.89 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 71 TYR 0.012 0.001 TYR A 659 PHE 0.013 0.001 PHE A 626 TRP 0.011 0.001 TRP A 466 HIS 0.003 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (10545) covalent geometry : angle 0.50007 / 0.28 (14364) hydrogen bonds : bond 0.04367 / 2.80 ( 485) hydrogen bonds : angle 4.26286 / 3.07 ( 1380) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 797 MET cc_start: 0.8478 (tmm) cc_final: 0.8014 (tmm) REVERT: A 845 GLU cc_start: 0.8136 (tp30) cc_final: 0.7901 (tp30) REVERT: A 897 TRP cc_start: 0.7580 (t-100) cc_final: 0.7331 (t-100) REVERT: A 1124 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8145 (mtpp) outliers start: 17 outliers final: 15 residues processed: 110 average time/residue: 0.1939 time to fit residues: 31.3216 Evaluate side-chains 108 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1089 ILE Chi-restraints excluded: chain A residue 1109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 111 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 434 HIS A 986 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.182797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136255 restraints weight = 40667.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136609 restraints weight = 27977.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138816 restraints weight = 27889.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140785 restraints weight = 17793.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142265 restraints weight = 15989.787| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10545 Z= 0.224 Angle : 0.533 5.381 14364 Z= 0.303 Chirality : 0.039 0.296 1613 Planarity : 0.003 0.049 1702 Dihedral : 18.769 177.395 1866 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.54 % Allowed : 10.89 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.26), residues: 1152 helix: 2.27 (0.23), residues: 547 sheet: 0.09 (0.49), residues: 117 loop : -0.99 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.013 0.002 TYR A 659 PHE 0.032 0.002 PHE A 915 TRP 0.012 0.001 TRP A 466 HIS 0.005 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (10545) covalent geometry : angle 0.53346 / 0.30 (14364) hydrogen bonds : bond 0.04823 / 3.08 ( 485) hydrogen bonds : angle 4.37495 / 3.14 ( 1380) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 797 MET cc_start: 0.8587 (tmm) cc_final: 0.8136 (tmm) REVERT: A 845 GLU cc_start: 0.8182 (tp30) cc_final: 0.7930 (tp30) REVERT: A 1124 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8150 (mtpp) outliers start: 16 outliers final: 15 residues processed: 106 average time/residue: 0.2037 time to fit residues: 31.1260 Evaluate side-chains 105 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1089 ILE Chi-restraints excluded: chain A residue 1109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 27 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.181776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135223 restraints weight = 40741.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135614 restraints weight = 27923.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137941 restraints weight = 27798.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139236 restraints weight = 17641.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.142958 restraints weight = 16128.814| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10545 Z= 0.218 Angle : 0.542 7.115 14364 Z= 0.308 Chirality : 0.040 0.302 1613 Planarity : 0.003 0.049 1702 Dihedral : 18.812 177.700 1866 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.64 % Allowed : 10.89 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.26), residues: 1152 helix: 2.08 (0.23), residues: 545 sheet: -0.00 (0.50), residues: 117 loop : -1.10 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1147 TYR 0.013 0.002 TYR A 659 PHE 0.037 0.002 PHE A 915 TRP 0.013 0.002 TRP A 387 HIS 0.005 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (10545) covalent geometry : angle 0.54244 / 0.31 (14364) hydrogen bonds : bond 0.04981 / 3.16 ( 485) hydrogen bonds : angle 4.41999 / 3.17 ( 1380) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 GLU cc_start: 0.8492 (tt0) cc_final: 0.8276 (tt0) REVERT: A 380 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.6036 (ttm) REVERT: A 403 LYS cc_start: 0.9101 (tptp) cc_final: 0.8504 (tppp) REVERT: A 797 MET cc_start: 0.8559 (tmm) cc_final: 0.8133 (tmm) REVERT: A 1124 LYS cc_start: 0.8574 (mmmt) cc_final: 0.8145 (mtpp) outliers start: 17 outliers final: 15 residues processed: 103 average time/residue: 0.1701 time to fit residues: 26.1706 Evaluate side-chains 106 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1089 ILE Chi-restraints excluded: chain A residue 1109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 0.0070 chunk 112 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.184754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.138429 restraints weight = 40724.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138598 restraints weight = 31132.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141986 restraints weight = 25863.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142621 restraints weight = 16913.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143318 restraints weight = 16220.977| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10545 Z= 0.105 Angle : 0.479 5.194 14364 Z= 0.269 Chirality : 0.038 0.271 1613 Planarity : 0.003 0.043 1702 Dihedral : 18.682 177.210 1866 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.16 % Allowed : 11.66 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.26), residues: 1152 helix: 2.25 (0.23), residues: 548 sheet: 0.11 (0.50), residues: 117 loop : -0.99 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1056 TYR 0.017 0.001 TYR A 326 PHE 0.044 0.001 PHE A 915 TRP 0.014 0.001 TRP A 897 HIS 0.003 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (10545) covalent geometry : angle 0.47891 / 0.27 (14364) hydrogen bonds : bond 0.04203 / 2.67 ( 485) hydrogen bonds : angle 4.18216 / 3.02 ( 1380) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 GLU cc_start: 0.8458 (tt0) cc_final: 0.8240 (tt0) REVERT: A 403 LYS cc_start: 0.9069 (tptp) cc_final: 0.8452 (tppp) REVERT: A 797 MET cc_start: 0.8517 (tmm) cc_final: 0.8069 (tmm) REVERT: A 1124 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8134 (mtpp) outliers start: 12 outliers final: 12 residues processed: 102 average time/residue: 0.1669 time to fit residues: 25.0912 Evaluate side-chains 102 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1073 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 33 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.182864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136456 restraints weight = 40681.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136599 restraints weight = 31193.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140104 restraints weight = 26287.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140540 restraints weight = 17163.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141255 restraints weight = 16479.026| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10545 Z= 0.174 Angle : 0.500 5.222 14364 Z= 0.284 Chirality : 0.038 0.288 1613 Planarity : 0.003 0.048 1702 Dihedral : 18.690 177.144 1866 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.75 % Rotamer: Outliers : 1.25 % Allowed : 11.56 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.26), residues: 1152 helix: 2.21 (0.23), residues: 547 sheet: 0.08 (0.50), residues: 117 loop : -1.08 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 768 TYR 0.014 0.001 TYR A 326 PHE 0.029 0.001 PHE A 915 TRP 0.012 0.001 TRP A 466 HIS 0.003 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (10545) covalent geometry : angle 0.50022 / 0.28 (14364) hydrogen bonds : bond 0.04538 / 2.87 ( 485) hydrogen bonds : angle 4.25247 / 3.06 ( 1380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2460.22 seconds wall clock time: 42 minutes 49.07 seconds (2569.07 seconds total)