Starting phenix.real_space_refine on Sat Jul 4 13:23:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hlx_52275/07_2026/9hlx_52275.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hlx_52275/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9hlx_52275/07_2026/9hlx_52275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hlx_52275/07_2026/9hlx_52275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hlx_52275/07_2026/9hlx_52275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hlx_52275/07_2026/9hlx_52275.map" } 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-dev-6108/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: 2.76, per 1000 atoms: 0.14 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: 1.71 Conformation dependent library (CDL) restraints added in 584.2 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: 2.81 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: 4.62 Time building geometry restraints manager: 2.44 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: 27242 2.60 - 5.21: 6439 5.21 - 7.81: 2846 7.81 - 10.41: 486 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: 935 0.149 - 0.299: 46 0.299 - 0.448: 113 0.448 - 0.597: 406 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: 1.480 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: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.020 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.410 ------------------------------------------------------------------------------- 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= 1.995 Angle : 2.815 12.660 14364 Z= 1.917 Chirality : 0.345 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 0.03739 / 1.99 (10545) covalent geometry : angle 2.81498 / 1.92 (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 : 0.479 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: 0.7985 (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: 0.2314 time to fit residues: 60.8081 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 : 0.414 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.187476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138351 restraints weight = 41606.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139754 restraints weight = 28343.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.141942 restraints weight = 22726.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.142684 restraints weight = 16283.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.143499 restraints weight = 15300.938| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10545 Z= 0.157 Angle : 0.626 6.919 14364 Z= 0.362 Chirality : 0.041 0.275 1613 Planarity : 0.004 0.044 1702 Dihedral : 18.711 176.995 1871 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.25 % Allowed : 8.77 % Favored : 89.98 % 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: 1.08 (0.25), residues: 1152 helix: 2.09 (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 0.004 0.000 ARG A 639 TYR 0.022 0.002 TYR A 659 PHE 0.019 0.001 PHE A 935 TRP 0.005 0.001 TRP A 466 HIS 0.007 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (10545) covalent geometry : angle 0.62554 / 0.36 (14364) hydrogen bonds : bond 0.05564 / 3.51 ( 485) hydrogen bonds : angle 5.03717 / 3.66 ( 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 146 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.427 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: 0.8641 (t70) cc_final: 0.8094 (t0) REVERT: A 72 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7348 (tm-30) REVERT: A 178 ASN cc_start: 0.9022 (p0) cc_final: 0.8718 (p0) REVERT: A 387 TRP cc_start: 0.9140 (t-100) cc_final: 0.8853 (t-100) REVERT: A 545 GLN cc_start: 0.8091 (tp40) cc_final: 0.7889 (tp-100) REVERT: A 679 LYS cc_start: 0.8137 (tptm) cc_final: 0.7707 (ttpt) REVERT: A 797 MET cc_start: 0.8545 (tmm) cc_final: 0.8245 (tmm) REVERT: A 845 GLU cc_start: 0.8117 (tp30) cc_final: 0.7832 (tp30) REVERT: A 979 TYR cc_start: 0.6104 (m-80) cc_final: 0.4910 (m-10) REVERT: A 1124 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8189 (mtpp) outliers start: 13 outliers final: 7 residues processed: 142 average time/residue: 0.1978 time to fit residues: 39.8891 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 : 0.526 ------------------------------------------------------------------------------- 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: 0.9980 chunk 94 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.195747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145190 restraints weight = 41526.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.146022 restraints weight = 28223.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.148316 restraints weight = 25698.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.149349 restraints weight = 17594.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.149923 restraints weight = 16085.200| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10545 Z= 0.146 Angle : 0.531 6.440 14364 Z= 0.308 Chirality : 0.038 0.194 1613 Planarity : 0.003 0.042 1702 Dihedral : 18.729 176.944 1866 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.25 % Allowed : 9.83 % Favored : 88.92 % 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: 1.35 (0.26), residues: 1152 helix: 2.46 (0.23), residues: 538 sheet: 0.63 (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 979 PHE 0.020 0.001 PHE A 935 TRP 0.009 0.001 TRP A 466 HIS 0.013 0.001 HIS A 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (10545) covalent geometry : angle 0.53097 / 0.31 (14364) hydrogen bonds : bond 0.04813 / 3.02 ( 485) hydrogen bonds : angle 4.66965 / 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 : 0.610 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: 0.8290 (t0) cc_final: 0.7890 (t0) REVERT: A 47 ASP cc_start: 0.8548 (t70) cc_final: 0.8009 (t0) REVERT: A 72 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7370 (tm-30) REVERT: A 178 ASN cc_start: 0.9046 (p0) cc_final: 0.8784 (p0) REVERT: A 387 TRP cc_start: 0.9118 (t-100) cc_final: 0.8855 (t-100) REVERT: A 403 LYS cc_start: 0.8842 (tppp) cc_final: 0.8339 (tppp) REVERT: A 797 MET cc_start: 0.8505 (tmm) cc_final: 0.8225 (tmm) REVERT: A 845 GLU cc_start: 0.8002 (tp30) cc_final: 0.7721 (tp30) REVERT: A 979 TYR cc_start: 0.5626 (m-80) cc_final: 0.5108 (m-80) REVERT: A 1124 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8134 (mtpp) outliers start: 13 outliers final: 10 residues processed: 124 average time/residue: 0.1780 time to fit residues: 32.3600 Evaluate side-chains 117 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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: 2.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 64 optimal weight: 0.0050 chunk 20 optimal weight: 0.1980 chunk 41 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.6400 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.194588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144485 restraints weight = 41613.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.145011 restraints weight = 30344.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.148359 restraints weight = 24596.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.148576 restraints weight = 17745.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.149193 restraints weight = 15985.305| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10545 Z= 0.150 Angle : 0.504 5.935 14364 Z= 0.292 Chirality : 0.037 0.178 1613 Planarity : 0.003 0.043 1702 Dihedral : 18.715 175.424 1866 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.35 % Allowed : 9.73 % Favored : 88.92 % 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: 1.38 (0.26), residues: 1152 helix: 2.51 (0.23), residues: 538 sheet: 0.52 (0.50), residues: 116 loop : -0.82 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 954 TYR 0.012 0.001 TYR A 659 PHE 0.015 0.001 PHE A 935 TRP 0.010 0.001 TRP A 466 HIS 0.005 0.001 HIS A 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (10545) covalent geometry : angle 0.50427 / 0.29 (14364) hydrogen bonds : bond 0.04471 / 2.83 ( 485) hydrogen bonds : angle 4.52147 / 3.27 ( 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: 14 poor density : 108 time to evaluate : 0.490 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: A 18 ASN cc_start: 0.8327 (t0) cc_final: 0.7993 (t0) REVERT: A 47 ASP cc_start: 0.8626 (t70) cc_final: 0.8006 (t0) REVERT: A 387 TRP cc_start: 0.9116 (t-100) cc_final: 0.8831 (t-100) REVERT: A 403 LYS cc_start: 0.8848 (tptp) cc_final: 0.8340 (tppp) REVERT: A 797 MET cc_start: 0.8491 (tmm) cc_final: 0.8033 (tmm) REVERT: A 845 GLU cc_start: 0.8038 (tp30) cc_final: 0.7755 (tp30) REVERT: A 1124 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8149 (mtpp) outliers start: 14 outliers final: 11 residues processed: 119 average time/residue: 0.1769 time to fit residues: 31.2399 Evaluate side-chains 114 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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: 1.9990 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: 2.9990 chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.196161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.143988 restraints weight = 41131.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148220 restraints weight = 28284.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.149909 restraints weight = 19884.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152875 restraints weight = 15210.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.153020 restraints weight = 13199.212| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10545 Z= 0.149 Angle : 0.487 5.707 14364 Z= 0.282 Chirality : 0.037 0.174 1613 Planarity : 0.003 0.046 1702 Dihedral : 18.708 175.905 1866 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.25 % Allowed : 9.83 % Favored : 88.92 % 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: 1.38 (0.26), residues: 1152 helix: 2.53 (0.23), residues: 544 sheet: 0.40 (0.50), residues: 116 loop : -0.87 (0.29), residues: 492 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 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 0.00335 / 0.15 (10545) covalent geometry : angle 0.48737 / 0.28 (14364) hydrogen bonds : bond 0.04343 / 2.77 ( 485) hydrogen bonds : angle 4.36392 / 3.15 ( 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 115 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 TRP cc_start: 0.9087 (t-100) cc_final: 0.8829 (t-100) REVERT: A 403 LYS cc_start: 0.8912 (tptp) cc_final: 0.8330 (tppp) REVERT: A 797 MET cc_start: 0.8505 (tmm) cc_final: 0.8016 (tmm) REVERT: A 845 GLU cc_start: 0.8061 (tp30) cc_final: 0.7785 (tp30) REVERT: A 1124 LYS cc_start: 0.8527 (mmmt) cc_final: 0.8126 (mtpp) outliers start: 13 outliers final: 11 residues processed: 111 average time/residue: 0.2039 time to fit residues: 32.7912 Evaluate side-chains 108 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 1109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 33 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.185726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.139442 restraints weight = 40253.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139811 restraints weight = 27863.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144250 restraints weight = 23386.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144367 restraints weight = 15527.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145773 restraints weight = 14905.121| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3003 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= 0.144 Angle : 0.485 6.759 14364 Z= 0.278 Chirality : 0.037 0.173 1613 Planarity : 0.003 0.045 1702 Dihedral : 18.659 176.108 1866 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.25 % Allowed : 10.40 % 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: 1.41 (0.26), residues: 1152 helix: 2.56 (0.23), residues: 545 sheet: 0.33 (0.49), 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 0.020 0.001 TYR A 326 PHE 0.016 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 0.00327 / 0.14 (10545) covalent geometry : angle 0.48507 / 0.28 (14364) hydrogen bonds : bond 0.04204 / 2.70 ( 485) hydrogen bonds : angle 4.25827 / 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: 13 poor density : 100 time to evaluate : 0.585 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: 0.9076 (t-100) cc_final: 0.8825 (t-100) REVERT: A 797 MET cc_start: 0.8482 (tmm) cc_final: 0.8024 (tmm) REVERT: A 845 GLU cc_start: 0.8107 (tp30) cc_final: 0.7836 (tp30) REVERT: A 1124 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8135 (mtpp) outliers start: 13 outliers final: 11 residues processed: 110 average time/residue: 0.2220 time to fit residues: 35.1753 Evaluate side-chains 105 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 1089 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 90 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 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 = 0.4169 r_free = 0.4169 target = 0.184694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137710 restraints weight = 40543.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141575 restraints weight = 28633.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.142997 restraints weight = 23267.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.143931 restraints weight = 16443.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144478 restraints weight = 15615.898| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10545 Z= 0.167 Angle : 0.486 5.241 14364 Z= 0.281 Chirality : 0.037 0.174 1613 Planarity : 0.003 0.048 1702 Dihedral : 18.654 176.615 1866 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.45 % Allowed : 10.21 % 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: 1.33 (0.26), residues: 1152 helix: 2.50 (0.23), residues: 546 sheet: 0.25 (0.49), residues: 117 loop : -0.88 (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 0.012 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 0.00384 / 0.17 (10545) covalent geometry : angle 0.48599 / 0.28 (14364) hydrogen bonds : bond 0.04326 / 2.77 ( 485) hydrogen bonds : angle 4.26175 / 3.06 ( 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 112 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.561 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 387 TRP cc_start: 0.9040 (t-100) cc_final: 0.8804 (t-100) REVERT: A 797 MET cc_start: 0.8489 (tmm) cc_final: 0.8021 (tmm) REVERT: A 845 GLU cc_start: 0.8141 (tp30) cc_final: 0.7903 (tp30) REVERT: A 1124 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8142 (mtpp) outliers start: 15 outliers final: 13 residues processed: 108 average time/residue: 0.1835 time to fit residues: 29.3405 Evaluate side-chains 107 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 1073 SER Chi-restraints excluded: chain A residue 1089 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 111 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.194591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144501 restraints weight = 41195.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149655 restraints weight = 27845.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.151260 restraints weight = 19166.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.151602 restraints weight = 14644.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152054 restraints weight = 14462.889| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10545 Z= 0.145 Angle : 0.478 5.952 14364 Z= 0.274 Chirality : 0.036 0.170 1613 Planarity : 0.003 0.046 1702 Dihedral : 18.629 176.871 1866 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.35 % Allowed : 10.89 % Favored : 87.76 % 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: 1.33 (0.26), residues: 1152 helix: 2.47 (0.23), residues: 546 sheet: 0.25 (0.50), residues: 117 loop : -0.85 (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 326 PHE 0.032 0.001 PHE A 915 TRP 0.012 0.001 TRP A 466 HIS 0.003 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (10545) covalent geometry : angle 0.47838 / 0.27 (14364) hydrogen bonds : bond 0.04191 / 2.68 ( 485) hydrogen bonds : angle 4.20454 / 3.02 ( 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 109 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.484 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: A 387 TRP cc_start: 0.9054 (t-100) cc_final: 0.8800 (t-100) REVERT: A 797 MET cc_start: 0.8502 (tmm) cc_final: 0.8028 (tmm) REVERT: A 845 GLU cc_start: 0.8148 (tp30) cc_final: 0.7878 (tp30) REVERT: A 1124 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8162 (mtpp) outliers start: 14 outliers final: 14 residues processed: 105 average time/residue: 0.1787 time to fit residues: 27.9000 Evaluate side-chains 106 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 27 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 85 optimal weight: 0.0020 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 overall best weight: 0.8390 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.186730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.139808 restraints weight = 40492.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143550 restraints weight = 28150.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145068 restraints weight = 22686.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146010 restraints weight = 16285.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.146583 restraints weight = 15406.978| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 10545 Z= 0.101 Angle : 0.453 5.194 14364 Z= 0.258 Chirality : 0.036 0.168 1613 Planarity : 0.003 0.045 1702 Dihedral : 18.518 176.882 1866 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.14 % Rotamer: Outliers : 1.25 % Allowed : 11.08 % Favored : 87.67 % 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: 1.47 (0.26), residues: 1152 helix: 2.56 (0.23), residues: 549 sheet: 0.32 (0.50), residues: 117 loop : -0.76 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 768 TYR 0.011 0.001 TYR A 326 PHE 0.010 0.001 PHE A 33 TRP 0.012 0.001 TRP A 466 HIS 0.002 0.001 HIS A 955 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (10545) covalent geometry : angle 0.45325 / 0.26 (14364) hydrogen bonds : bond 0.03719 / 2.38 ( 485) hydrogen bonds : angle 4.04356 / 2.92 ( 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 110 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.459 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 797 MET cc_start: 0.8460 (tmm) cc_final: 0.7991 (tmm) REVERT: A 845 GLU cc_start: 0.8082 (tp30) cc_final: 0.7836 (tp30) REVERT: A 1124 LYS cc_start: 0.8546 (mmmt) cc_final: 0.8137 (mtpp) outliers start: 13 outliers final: 13 residues processed: 107 average time/residue: 0.2124 time to fit residues: 32.3460 Evaluate side-chains 104 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 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 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: 6.9990 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 0.0370 chunk 112 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.5864 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.195044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143940 restraints weight = 41603.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.148438 restraints weight = 29697.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.150744 restraints weight = 19595.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151177 restraints weight = 14425.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.151551 restraints weight = 13924.808| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10545 Z= 0.143 Angle : 0.469 5.068 14364 Z= 0.268 Chirality : 0.036 0.167 1613 Planarity : 0.003 0.046 1702 Dihedral : 18.530 177.173 1866 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.21 % Favored : 94.70 % Rotamer: Outliers : 1.25 % Allowed : 11.27 % 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: 1.41 (0.26), residues: 1152 helix: 2.55 (0.23), residues: 546 sheet: 0.29 (0.49), residues: 117 loop : -0.82 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 768 TYR 0.010 0.001 TYR A 326 PHE 0.013 0.001 PHE A 915 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 0.00330 / 0.14 (10545) covalent geometry : angle 0.46922 / 0.27 (14364) hydrogen bonds : bond 0.03965 / 2.52 ( 485) hydrogen bonds : angle 4.07529 / 2.93 ( 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 108 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.571 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: A 797 MET cc_start: 0.8527 (tmm) cc_final: 0.8066 (tmm) REVERT: A 845 GLU cc_start: 0.8110 (tp30) cc_final: 0.7883 (tp30) REVERT: A 1124 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8136 (mtpp) outliers start: 13 outliers final: 12 residues processed: 105 average time/residue: 0.2227 time to fit residues: 34.4541 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 : 0.569 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 85 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.185173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139325 restraints weight = 40789.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139549 restraints weight = 30861.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142637 restraints weight = 26375.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143707 restraints weight = 16511.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144328 restraints weight = 15620.759| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10545 Z= 0.132 Angle : 0.469 5.892 14364 Z= 0.267 Chirality : 0.036 0.166 1613 Planarity : 0.003 0.046 1702 Dihedral : 18.527 177.383 1866 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 1.16 % Allowed : 11.56 % Favored : 87.28 % 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: 1.32 (0.26), residues: 1152 helix: 2.45 (0.23), residues: 546 sheet: 0.27 (0.50), residues: 117 loop : -0.83 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 768 TYR 0.010 0.001 TYR A 326 PHE 0.036 0.001 PHE A 915 TRP 0.020 0.001 TRP A 387 HIS 0.003 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10545) covalent geometry : angle 0.46859 / 0.27 (14364) hydrogen bonds : bond 0.03955 / 2.50 ( 485) hydrogen bonds : angle 4.07749 / 2.94 ( 1380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2614.12 seconds wall clock time: 45 minutes 24.77 seconds (2724.77 seconds total)