Starting phenix.real_space_refine on Wed Jun 18 17:34:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7usc_26732/06_2025/7usc_26732.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usc_26732/06_2025/7usc_26732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7usc_26732/06_2025/7usc_26732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usc_26732/06_2025/7usc_26732.map" model { file = "/net/cci-nas-00/data/ceres_data/7usc_26732/06_2025/7usc_26732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usc_26732/06_2025/7usc_26732.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 146 5.16 5 C 13831 2.51 5 N 3709 2.21 5 O 4023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21709 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9693 Classifications: {'peptide': 1183} Link IDs: {'PTRANS': 44, 'TRANS': 1138} Chain breaks: 6 Chain: "B" Number of atoms: 8716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8716 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 36, 'TRANS': 1050} Chain breaks: 3 Chain: "C" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1570 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain breaks: 2 Chain: "D" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 502 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "E" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1228 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 4, 'TRANS': 148} Time building chain proxies: 11.84, per 1000 atoms: 0.55 Number of scatterers: 21709 At special positions: 0 Unit cell: (140.988, 141.863, 209.292, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 146 16.00 O 4023 8.00 N 3709 7.00 C 13831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.68 Conformation dependent library (CDL) restraints added in 3.0 seconds 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5176 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 7 sheets defined 77.0% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 6 through 18 Processing helix chain 'A' and resid 58 through 85 removed outlier: 4.057A pdb=" N GLN A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 144 removed outlier: 4.072A pdb=" N LYS A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Proline residue: A 117 - end of helix Processing helix chain 'A' and resid 146 through 151 removed outlier: 3.718A pdb=" N LYS A 150 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 178 Processing helix chain 'A' and resid 179 through 195 removed outlier: 3.656A pdb=" N ASN A 183 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 216 Processing helix chain 'A' and resid 218 through 229 Processing helix chain 'A' and resid 234 through 252 removed outlier: 3.653A pdb=" N LEU A 238 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 275 removed outlier: 3.649A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 291 through 302 removed outlier: 3.517A pdb=" N ILE A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 321 removed outlier: 4.153A pdb=" N ILE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 332 removed outlier: 5.366A pdb=" N SER A 330 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A 332 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 347 Processing helix chain 'A' and resid 348 through 364 removed outlier: 3.532A pdb=" N GLU A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.687A pdb=" N TYR A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 440 through 443 removed outlier: 4.252A pdb=" N TYR A 443 " --> pdb=" O ARG A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 444 through 468 removed outlier: 3.618A pdb=" N MET A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 491 Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'A' and resid 530 through 535 removed outlier: 3.836A pdb=" N ARG A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.922A pdb=" N SER A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 584' Processing helix chain 'A' and resid 585 through 599 removed outlier: 3.578A pdb=" N ILE A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 607 removed outlier: 3.563A pdb=" N ASN A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 removed outlier: 3.616A pdb=" N CYS A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 removed outlier: 5.654A pdb=" N GLN A 620 " --> pdb=" O ASP A 617 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 621 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP A 622 " --> pdb=" O SER A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 622' Processing helix chain 'A' and resid 624 through 631 removed outlier: 3.596A pdb=" N THR A 631 " --> pdb=" O PHE A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 642 Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 658 through 662 removed outlier: 4.304A pdb=" N GLU A 662 " --> pdb=" O SER A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 681 removed outlier: 3.650A pdb=" N SER A 667 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASN A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 722 removed outlier: 3.790A pdb=" N TYR A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 734 Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 763 through 789 removed outlier: 3.617A pdb=" N LEU A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 793 No H-bonds generated for 'chain 'A' and resid 791 through 793' Processing helix chain 'A' and resid 794 through 814 removed outlier: 3.734A pdb=" N ARG A 814 " --> pdb=" O LYS A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 829 Processing helix chain 'A' and resid 837 through 851 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 891 through 903 Processing helix chain 'A' and resid 904 through 906 No H-bonds generated for 'chain 'A' and resid 904 through 906' Processing helix chain 'A' and resid 910 through 942 removed outlier: 7.563A pdb=" N TYR A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLN A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 956 Processing helix chain 'A' and resid 964 through 967 Processing helix chain 'A' and resid 968 through 980 Processing helix chain 'A' and resid 980 through 985 Processing helix chain 'A' and resid 992 through 1026 removed outlier: 3.607A pdb=" N CYS A1020 " --> pdb=" O LEU A1016 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1030 removed outlier: 3.771A pdb=" N ASN A1030 " --> pdb=" O PRO A1027 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1027 through 1030' Processing helix chain 'A' and resid 1042 through 1055 Processing helix chain 'A' and resid 1058 through 1067 removed outlier: 3.722A pdb=" N LEU A1062 " --> pdb=" O HIS A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1084 removed outlier: 3.525A pdb=" N GLU A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1102 Processing helix chain 'A' and resid 1126 through 1139 removed outlier: 3.587A pdb=" N LEU A1130 " --> pdb=" O GLU A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1153 Processing helix chain 'A' and resid 1155 through 1168 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1178 through 1191 Processing helix chain 'A' and resid 1200 through 1226 Processing helix chain 'B' and resid 12 through 38 removed outlier: 3.532A pdb=" N ASP B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.551A pdb=" N ILE B 49 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.655A pdb=" N LYS B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 82 through 90 removed outlier: 3.846A pdb=" N LYS B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 118 Processing helix chain 'B' and resid 126 through 149 Processing helix chain 'B' and resid 152 through 169 Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.522A pdb=" N LYS B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.673A pdb=" N MET B 239 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.651A pdb=" N TYR B 252 " --> pdb=" O PRO B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 269 Processing helix chain 'B' and resid 270 through 273 Processing helix chain 'B' and resid 276 through 289 removed outlier: 3.512A pdb=" N LEU B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 313 removed outlier: 4.515A pdb=" N ASN B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 360 removed outlier: 3.646A pdb=" N ASN B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLY B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 367 through 391 removed outlier: 3.526A pdb=" N VAL B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 422 removed outlier: 3.788A pdb=" N LEU B 408 " --> pdb=" O HIS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 448 removed outlier: 3.759A pdb=" N MET B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ALA B 439 " --> pdb=" O SER B 435 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 469 Processing helix chain 'B' and resid 471 through 478 removed outlier: 3.922A pdb=" N VAL B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 499 removed outlier: 3.799A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 508 removed outlier: 3.666A pdb=" N ASP B 508 " --> pdb=" O GLY B 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 505 through 508' Processing helix chain 'B' and resid 509 through 528 removed outlier: 3.502A pdb=" N GLY B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 537 Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.543A pdb=" N PHE B 542 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 removed outlier: 3.577A pdb=" N LEU B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'B' and resid 567 through 573 removed outlier: 3.651A pdb=" N CYS B 573 " --> pdb=" O PHE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 580 removed outlier: 4.461A pdb=" N MET B 577 " --> pdb=" O THR B 574 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR B 580 " --> pdb=" O MET B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 626 removed outlier: 4.708A pdb=" N HIS B 589 " --> pdb=" O PRO B 585 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 632 Processing helix chain 'B' and resid 633 through 643 Processing helix chain 'B' and resid 673 through 690 removed outlier: 3.829A pdb=" N SER B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 724 removed outlier: 3.996A pdb=" N TYR B 707 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 708 " --> pdb=" O PRO B 704 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR B 724 " --> pdb=" O ILE B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 752 Processing helix chain 'B' and resid 753 through 756 Processing helix chain 'B' and resid 760 through 772 removed outlier: 3.923A pdb=" N VAL B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 772 " --> pdb=" O VAL B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 795 Processing helix chain 'B' and resid 795 through 803 Processing helix chain 'B' and resid 827 through 832 Processing helix chain 'B' and resid 832 through 872 Proline residue: B 845 - end of helix removed outlier: 3.803A pdb=" N HIS B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 881 Processing helix chain 'B' and resid 886 through 896 removed outlier: 3.743A pdb=" N ARG B 896 " --> pdb=" O ALA B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 932 removed outlier: 3.765A pdb=" N VAL B 903 " --> pdb=" O SER B 899 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR B 930 " --> pdb=" O ASP B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 945 Processing helix chain 'B' and resid 951 through 966 removed outlier: 3.596A pdb=" N ASN B 957 " --> pdb=" O LYS B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 979 Processing helix chain 'B' and resid 989 through 1006 Processing helix chain 'B' and resid 1008 through 1013 removed outlier: 4.362A pdb=" N SER B1012 " --> pdb=" O PRO B1008 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1008 through 1013' Processing helix chain 'B' and resid 1028 through 1030 No H-bonds generated for 'chain 'B' and resid 1028 through 1030' Processing helix chain 'B' and resid 1031 through 1047 Processing helix chain 'B' and resid 1050 through 1071 removed outlier: 3.893A pdb=" N GLN B1071 " --> pdb=" O LEU B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1095 removed outlier: 3.821A pdb=" N LEU B1087 " --> pdb=" O SER B1083 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU B1088 " --> pdb=" O VAL B1084 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP B1089 " --> pdb=" O TYR B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1107 removed outlier: 3.685A pdb=" N LEU B1103 " --> pdb=" O THR B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1121 removed outlier: 4.067A pdb=" N LEU B1112 " --> pdb=" O PRO B1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 81 removed outlier: 3.948A pdb=" N VAL C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.576A pdb=" N PHE C 150 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 177 Processing helix chain 'C' and resid 500 through 515 Processing helix chain 'C' and resid 530 through 543 Processing helix chain 'D' and resid 11 through 68 Processing helix chain 'E' and resid 4 through 39 removed outlier: 3.751A pdb=" N GLU E 10 " --> pdb=" O MET E 6 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ILE E 12 " --> pdb=" O LEU E 8 " (cutoff:3.500A) Proline residue: E 13 - end of helix removed outlier: 3.874A pdb=" N ASP E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 110 Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing sheet with id=AA1, first strand: chain 'A' and resid 304 through 308 removed outlier: 5.980A pdb=" N ILE A 313 " --> pdb=" O PRO A 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 755 through 757 Processing sheet with id=AA3, first strand: chain 'A' and resid 855 through 858 Processing sheet with id=AA4, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AA5, first strand: chain 'B' and resid 695 through 697 Processing sheet with id=AA6, first strand: chain 'B' and resid 805 through 808 removed outlier: 3.502A pdb=" N ALA B 813 " --> pdb=" O PHE B 808 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1018 through 1019 1453 hydrogen bonds defined for protein. 4236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.23 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6965 1.33 - 1.45: 2765 1.45 - 1.57: 12161 1.57 - 1.69: 0 1.69 - 1.81: 237 Bond restraints: 22128 Sorted by residual: bond pdb=" C THR B 783 " pdb=" N ILE B 784 " ideal model delta sigma weight residual 1.335 1.243 0.091 1.15e-02 7.56e+03 6.31e+01 bond pdb=" C PRO C 131 " pdb=" N PRO C 132 " ideal model delta sigma weight residual 1.331 1.366 -0.034 8.70e-03 1.32e+04 1.57e+01 bond pdb=" N VAL B 300 " pdb=" CA VAL B 300 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.14e-02 7.69e+03 1.13e+01 bond pdb=" N LEU A 569 " pdb=" CA LEU A 569 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ILE C 95 " pdb=" CA ILE C 95 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.14e+00 ... (remaining 22123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 28774 1.40 - 2.81: 901 2.81 - 4.21: 170 4.21 - 5.61: 32 5.61 - 7.01: 4 Bond angle restraints: 29881 Sorted by residual: angle pdb=" C PHE A 638 " pdb=" N PRO A 639 " pdb=" CA PRO A 639 " ideal model delta sigma weight residual 119.85 124.83 -4.98 1.01e+00 9.80e-01 2.43e+01 angle pdb=" CA PRO C 131 " pdb=" C PRO C 131 " pdb=" N PRO C 132 " ideal model delta sigma weight residual 117.93 123.40 -5.47 1.20e+00 6.94e-01 2.08e+01 angle pdb=" C PHE A 164 " pdb=" N ILE A 165 " pdb=" CA ILE A 165 " ideal model delta sigma weight residual 120.46 114.35 6.11 1.37e+00 5.33e-01 1.99e+01 angle pdb=" N SER A 872 " pdb=" CA SER A 872 " pdb=" C SER A 872 " ideal model delta sigma weight residual 108.41 115.42 -7.01 1.63e+00 3.76e-01 1.85e+01 angle pdb=" N VAL C 127 " pdb=" CA VAL C 127 " pdb=" C VAL C 127 " ideal model delta sigma weight residual 113.22 108.24 4.98 1.23e+00 6.61e-01 1.64e+01 ... (remaining 29876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12146 17.92 - 35.84: 1165 35.84 - 53.76: 197 53.76 - 71.68: 25 71.68 - 89.60: 18 Dihedral angle restraints: 13551 sinusoidal: 5610 harmonic: 7941 Sorted by residual: dihedral pdb=" CA ASN B 187 " pdb=" C ASN B 187 " pdb=" N PRO B 188 " pdb=" CA PRO B 188 " ideal model delta harmonic sigma weight residual -180.00 -156.97 -23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA PHE B1044 " pdb=" C PHE B1044 " pdb=" N THR B1045 " pdb=" CA THR B1045 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ASN B 873 " pdb=" C ASN B 873 " pdb=" N VAL B 874 " pdb=" CA VAL B 874 " ideal model delta harmonic sigma weight residual 180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 13548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2805 0.053 - 0.106: 470 0.106 - 0.160: 83 0.160 - 0.213: 10 0.213 - 0.266: 5 Chirality restraints: 3373 Sorted by residual: chirality pdb=" CA LEU C 92 " pdb=" N LEU C 92 " pdb=" C LEU C 92 " pdb=" CB LEU C 92 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA HIS B 589 " pdb=" N HIS B 589 " pdb=" C HIS B 589 " pdb=" CB HIS B 589 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ILE A 570 " pdb=" N ILE A 570 " pdb=" C ILE A 570 " pdb=" CB ILE A 570 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 3370 not shown) Planarity restraints: 3811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 783 " 0.020 2.00e-02 2.50e+03 3.87e-02 1.49e+01 pdb=" C THR B 783 " -0.067 2.00e-02 2.50e+03 pdb=" O THR B 783 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE B 784 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.031 2.00e-02 2.50e+03 2.56e-02 1.14e+01 pdb=" CG PHE A 164 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 149 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" C ARG A 149 " 0.046 2.00e-02 2.50e+03 pdb=" O ARG A 149 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 150 " -0.016 2.00e-02 2.50e+03 ... (remaining 3808 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 356 2.68 - 3.24: 22119 3.24 - 3.79: 33630 3.79 - 4.35: 45518 4.35 - 4.90: 76114 Nonbonded interactions: 177737 Sorted by model distance: nonbonded pdb=" O ASP A 427 " pdb=" OD1 ASP A 427 " model vdw 2.130 3.040 nonbonded pdb=" ND2 ASN B 33 " pdb=" OE1 GLU B 587 " model vdw 2.205 3.120 nonbonded pdb=" O LYS A 594 " pdb=" OE1 GLU A 598 " model vdw 2.213 3.040 nonbonded pdb=" NH1 ARG A 964 " pdb=" OE1 GLN B 228 " model vdw 2.214 3.120 nonbonded pdb=" O ARG A 766 " pdb=" OG1 THR A 769 " model vdw 2.228 3.040 ... (remaining 177732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.010 Extract box with map and model: 0.950 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 46.130 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.080 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:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 : 0.007 0.091 22128 Z= 0.326 Angle : 0.617 7.014 29881 Z= 0.378 Chirality : 0.043 0.266 3373 Planarity : 0.004 0.047 3811 Dihedral : 14.115 89.602 8375 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.16), residues: 2641 helix: 1.54 (0.12), residues: 1884 sheet: -3.24 (0.82), residues: 32 loop : -0.49 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 16 HIS 0.006 0.001 HIS A1128 PHE 0.059 0.002 PHE A 164 TYR 0.017 0.002 TYR B 430 ARG 0.006 0.000 ARG A 919 Details of bonding type rmsd hydrogen bonds : bond 0.13029 ( 1453) hydrogen bonds : angle 4.65023 ( 4236) covalent geometry : bond 0.00679 (22128) covalent geometry : angle 0.61687 (29881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 2.413 Fit side-chains REVERT: A 82 MET cc_start: 0.9085 (tmm) cc_final: 0.8860 (tmm) REVERT: A 533 LEU cc_start: 0.8934 (mp) cc_final: 0.8714 (mm) REVERT: B 601 MET cc_start: 0.8222 (tmm) cc_final: 0.7750 (tmt) REVERT: C 109 GLN cc_start: 0.7665 (mt0) cc_final: 0.7257 (mt0) REVERT: D 49 THR cc_start: 0.9135 (m) cc_final: 0.8838 (p) REVERT: D 53 LYS cc_start: 0.8793 (tptt) cc_final: 0.8592 (mmmm) REVERT: E 108 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6792 (mt-10) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 1.7905 time to fit residues: 572.7688 Evaluate side-chains 195 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 241 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 89 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.081198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.067431 restraints weight = 45407.760| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.76 r_work: 0.2937 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 22128 Z= 0.239 Angle : 0.569 10.005 29881 Z= 0.306 Chirality : 0.041 0.192 3373 Planarity : 0.004 0.046 3811 Dihedral : 3.880 21.703 2922 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.36 % Allowed : 7.66 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.16), residues: 2641 helix: 1.98 (0.12), residues: 1874 sheet: -2.64 (0.88), residues: 32 loop : -0.24 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 646 HIS 0.007 0.001 HIS A1128 PHE 0.031 0.002 PHE B 549 TYR 0.023 0.002 TYR A1138 ARG 0.007 0.000 ARG E 45 Details of bonding type rmsd hydrogen bonds : bond 0.06750 ( 1453) hydrogen bonds : angle 3.98402 ( 4236) covalent geometry : bond 0.00560 (22128) covalent geometry : angle 0.56944 (29881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 2.747 Fit side-chains REVERT: A 208 GLN cc_start: 0.8659 (tp40) cc_final: 0.8036 (tp40) REVERT: A 533 LEU cc_start: 0.9108 (mp) cc_final: 0.8886 (mm) REVERT: B 51 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8429 (mppt) REVERT: B 392 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6605 (pmm) REVERT: B 832 ASP cc_start: 0.7673 (t0) cc_final: 0.7470 (t70) REVERT: D 49 THR cc_start: 0.9216 (m) cc_final: 0.8767 (p) REVERT: D 53 LYS cc_start: 0.9168 (tptt) cc_final: 0.8920 (mmmm) REVERT: E 6 MET cc_start: 0.7543 (tmm) cc_final: 0.7150 (tmm) REVERT: E 74 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8088 (mp10) outliers start: 33 outliers final: 10 residues processed: 219 average time/residue: 1.7023 time to fit residues: 416.6986 Evaluate side-chains 208 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 33 CYS Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 94 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 97 optimal weight: 0.0570 chunk 225 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 GLN C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.082825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.069033 restraints weight = 44993.736| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.76 r_work: 0.2977 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22128 Z= 0.143 Angle : 0.502 16.896 29881 Z= 0.267 Chirality : 0.038 0.240 3373 Planarity : 0.004 0.047 3811 Dihedral : 3.684 19.755 2922 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.48 % Allowed : 9.15 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.17), residues: 2641 helix: 2.29 (0.12), residues: 1874 sheet: -2.38 (0.87), residues: 32 loop : -0.11 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.005 0.001 HIS A1128 PHE 0.020 0.001 PHE B 549 TYR 0.020 0.001 TYR A1138 ARG 0.005 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.05673 ( 1453) hydrogen bonds : angle 3.75049 ( 4236) covalent geometry : bond 0.00319 (22128) covalent geometry : angle 0.50236 (29881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 2.922 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8729 (tp40) cc_final: 0.8025 (tp40) REVERT: A 533 LEU cc_start: 0.9113 (mp) cc_final: 0.8887 (mm) REVERT: B 51 LYS cc_start: 0.8645 (mmmm) cc_final: 0.8419 (mppt) REVERT: B 305 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8174 (tptp) REVERT: B 392 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6561 (pmm) REVERT: D 49 THR cc_start: 0.9199 (m) cc_final: 0.8768 (p) REVERT: E 6 MET cc_start: 0.7837 (tmm) cc_final: 0.7460 (tmm) REVERT: E 36 ASN cc_start: 0.8229 (t0) cc_final: 0.7994 (t0) outliers start: 36 outliers final: 11 residues processed: 217 average time/residue: 1.6390 time to fit residues: 398.1295 Evaluate side-chains 205 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain E residue 33 CYS Chi-restraints excluded: chain E residue 129 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 227 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 259 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 228 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 210 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 854 ASN B 161 ASN C 109 GLN E 74 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.083355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.069349 restraints weight = 45551.196| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.84 r_work: 0.2980 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22128 Z= 0.130 Angle : 0.483 17.291 29881 Z= 0.254 Chirality : 0.037 0.188 3373 Planarity : 0.003 0.048 3811 Dihedral : 3.548 19.221 2922 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.03 % Allowed : 10.92 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.17), residues: 2641 helix: 2.44 (0.12), residues: 1882 sheet: -2.28 (0.86), residues: 32 loop : 0.02 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.005 0.001 HIS A1128 PHE 0.016 0.001 PHE B 549 TYR 0.030 0.001 TYR C 156 ARG 0.004 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.05275 ( 1453) hydrogen bonds : angle 3.64091 ( 4236) covalent geometry : bond 0.00288 (22128) covalent geometry : angle 0.48325 (29881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 2.462 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8754 (tp40) cc_final: 0.8087 (tp40) REVERT: A 533 LEU cc_start: 0.9111 (mp) cc_final: 0.8886 (mm) REVERT: A 546 LYS cc_start: 0.7425 (tmtt) cc_final: 0.7218 (ptmm) REVERT: B 51 LYS cc_start: 0.8634 (mmmm) cc_final: 0.8412 (mppt) REVERT: B 305 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8165 (tptp) REVERT: B 476 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: E 6 MET cc_start: 0.7752 (tmm) cc_final: 0.7461 (tmm) REVERT: E 36 ASN cc_start: 0.8223 (t0) cc_final: 0.8000 (t0) outliers start: 25 outliers final: 7 residues processed: 211 average time/residue: 1.6368 time to fit residues: 387.3198 Evaluate side-chains 204 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain E residue 94 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 47 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS A1215 ASN C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.081317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.067536 restraints weight = 45427.527| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.76 r_work: 0.2936 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22128 Z= 0.229 Angle : 0.546 17.065 29881 Z= 0.285 Chirality : 0.040 0.191 3373 Planarity : 0.004 0.046 3811 Dihedral : 3.631 21.016 2922 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.32 % Allowed : 11.91 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.17), residues: 2641 helix: 2.37 (0.12), residues: 1867 sheet: -2.31 (0.86), residues: 32 loop : -0.01 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 646 HIS 0.007 0.001 HIS A1128 PHE 0.021 0.002 PHE B1002 TYR 0.022 0.001 TYR A1138 ARG 0.006 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.06194 ( 1453) hydrogen bonds : angle 3.71968 ( 4236) covalent geometry : bond 0.00546 (22128) covalent geometry : angle 0.54622 (29881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 2.351 Fit side-chains revert: symmetry clash REVERT: A 164 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.9026 (m-80) REVERT: A 208 GLN cc_start: 0.8794 (tp40) cc_final: 0.8159 (tp40) REVERT: A 426 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8447 (mttm) REVERT: A 533 LEU cc_start: 0.9113 (mp) cc_final: 0.8881 (mm) REVERT: B 51 LYS cc_start: 0.8664 (mmmm) cc_final: 0.8448 (mppt) REVERT: B 297 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8798 (ptp-170) REVERT: B 305 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8270 (tptt) REVERT: B 476 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: E 6 MET cc_start: 0.7782 (tmm) cc_final: 0.7471 (tmm) REVERT: E 36 ASN cc_start: 0.8271 (t0) cc_final: 0.8016 (t0) outliers start: 32 outliers final: 12 residues processed: 217 average time/residue: 1.6973 time to fit residues: 412.4268 Evaluate side-chains 213 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 94 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 131 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 251 optimal weight: 0.0670 chunk 113 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 overall best weight: 0.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.084140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.070250 restraints weight = 45310.203| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.82 r_work: 0.2999 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 22128 Z= 0.113 Angle : 0.476 17.136 29881 Z= 0.249 Chirality : 0.037 0.184 3373 Planarity : 0.003 0.049 3811 Dihedral : 3.457 18.707 2922 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.95 % Allowed : 13.14 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.17), residues: 2641 helix: 2.52 (0.12), residues: 1895 sheet: -2.11 (0.90), residues: 32 loop : 0.14 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 646 HIS 0.004 0.001 HIS A1128 PHE 0.011 0.001 PHE A 391 TYR 0.030 0.001 TYR C 156 ARG 0.006 0.000 ARG E 45 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 1453) hydrogen bonds : angle 3.56406 ( 4236) covalent geometry : bond 0.00234 (22128) covalent geometry : angle 0.47584 (29881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8777 (tp40) cc_final: 0.8122 (tp40) REVERT: A 426 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8435 (mttm) REVERT: A 533 LEU cc_start: 0.9120 (mp) cc_final: 0.8894 (mm) REVERT: B 305 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8090 (tptp) REVERT: B 476 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: E 6 MET cc_start: 0.7835 (tmm) cc_final: 0.7497 (tmm) REVERT: E 36 ASN cc_start: 0.8203 (t0) cc_final: 0.7975 (t0) outliers start: 23 outliers final: 8 residues processed: 215 average time/residue: 1.8751 time to fit residues: 454.1494 Evaluate side-chains 203 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 193 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 94 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 150 optimal weight: 0.9990 chunk 237 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 30 optimal weight: 0.2980 chunk 130 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A1215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.082842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.068766 restraints weight = 45372.168| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.83 r_work: 0.2967 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22128 Z= 0.165 Angle : 0.507 16.587 29881 Z= 0.264 Chirality : 0.038 0.196 3373 Planarity : 0.003 0.047 3811 Dihedral : 3.452 19.641 2922 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.07 % Allowed : 13.80 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.17), residues: 2641 helix: 2.50 (0.12), residues: 1891 sheet: -2.17 (0.88), residues: 32 loop : 0.12 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.006 0.001 HIS A1128 PHE 0.014 0.001 PHE A 391 TYR 0.031 0.001 TYR C 156 ARG 0.007 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.05373 ( 1453) hydrogen bonds : angle 3.58684 ( 4236) covalent geometry : bond 0.00386 (22128) covalent geometry : angle 0.50731 (29881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8803 (tp40) cc_final: 0.8390 (tp40) REVERT: A 533 LEU cc_start: 0.9136 (mp) cc_final: 0.8908 (mm) REVERT: B 305 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8227 (tptt) REVERT: B 476 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: C 97 MET cc_start: 0.6949 (mmt) cc_final: 0.6505 (tmt) REVERT: E 6 MET cc_start: 0.7835 (tmm) cc_final: 0.7501 (tmm) REVERT: E 36 ASN cc_start: 0.8224 (t0) cc_final: 0.7978 (t0) outliers start: 26 outliers final: 12 residues processed: 216 average time/residue: 1.6796 time to fit residues: 407.7550 Evaluate side-chains 212 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain E residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 97 optimal weight: 0.4980 chunk 206 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 231 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A1215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.083791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069937 restraints weight = 45125.541| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.81 r_work: 0.2995 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 22128 Z= 0.123 Angle : 0.490 16.685 29881 Z= 0.255 Chirality : 0.037 0.195 3373 Planarity : 0.003 0.048 3811 Dihedral : 3.408 18.663 2922 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.82 % Allowed : 14.34 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.17), residues: 2641 helix: 2.58 (0.12), residues: 1887 sheet: -2.09 (0.88), residues: 32 loop : 0.15 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.004 0.001 HIS A1128 PHE 0.013 0.001 PHE A 391 TYR 0.026 0.001 TYR C 156 ARG 0.007 0.000 ARG E 45 Details of bonding type rmsd hydrogen bonds : bond 0.04920 ( 1453) hydrogen bonds : angle 3.54255 ( 4236) covalent geometry : bond 0.00273 (22128) covalent geometry : angle 0.48998 (29881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8939 (tp40) cc_final: 0.8428 (tp40) REVERT: A 426 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8476 (mttm) REVERT: A 533 LEU cc_start: 0.9133 (mp) cc_final: 0.8906 (mm) REVERT: B 305 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8148 (tptp) REVERT: B 476 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: B 531 GLU cc_start: 0.8119 (mp0) cc_final: 0.7867 (mp0) REVERT: C 97 MET cc_start: 0.6826 (mmt) cc_final: 0.6529 (tmt) REVERT: E 6 MET cc_start: 0.7856 (tmm) cc_final: 0.7521 (tmm) REVERT: E 36 ASN cc_start: 0.8236 (t0) cc_final: 0.7994 (t0) outliers start: 20 outliers final: 10 residues processed: 210 average time/residue: 1.6717 time to fit residues: 394.2318 Evaluate side-chains 208 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain E residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 12 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 193 optimal weight: 0.2980 chunk 125 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.084913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.071017 restraints weight = 44964.324| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.80 r_work: 0.3018 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 22128 Z= 0.111 Angle : 0.488 16.514 29881 Z= 0.254 Chirality : 0.037 0.184 3373 Planarity : 0.003 0.048 3811 Dihedral : 3.337 17.703 2922 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.58 % Allowed : 14.63 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.17), residues: 2641 helix: 2.63 (0.12), residues: 1894 sheet: -2.07 (0.85), residues: 32 loop : 0.22 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 646 HIS 0.004 0.001 HIS A1128 PHE 0.012 0.001 PHE A 391 TYR 0.019 0.001 TYR A1138 ARG 0.007 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.04550 ( 1453) hydrogen bonds : angle 3.49479 ( 4236) covalent geometry : bond 0.00240 (22128) covalent geometry : angle 0.48778 (29881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.8048 (mpt180) cc_final: 0.7819 (mmt-90) REVERT: A 208 GLN cc_start: 0.8913 (tp40) cc_final: 0.8395 (tp40) REVERT: A 426 LYS cc_start: 0.8847 (mmmt) cc_final: 0.8453 (mttp) REVERT: A 533 LEU cc_start: 0.9158 (mp) cc_final: 0.8944 (mm) REVERT: B 305 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8072 (tptp) REVERT: B 476 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: C 97 MET cc_start: 0.6868 (mmt) cc_final: 0.6509 (tmt) REVERT: C 143 ASP cc_start: 0.8288 (m-30) cc_final: 0.8086 (t0) REVERT: C 503 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: E 6 MET cc_start: 0.7905 (tmm) cc_final: 0.7569 (tmm) REVERT: E 36 ASN cc_start: 0.8095 (t0) cc_final: 0.7851 (t0) outliers start: 14 outliers final: 10 residues processed: 211 average time/residue: 1.7369 time to fit residues: 411.8593 Evaluate side-chains 204 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 503 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain E residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 133 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 232 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 261 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 225 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.085418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.071630 restraints weight = 45261.926| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.76 r_work: 0.3032 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 22128 Z= 0.112 Angle : 0.493 16.369 29881 Z= 0.256 Chirality : 0.037 0.184 3373 Planarity : 0.003 0.047 3811 Dihedral : 3.307 17.440 2922 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.74 % Allowed : 14.71 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.17), residues: 2641 helix: 2.67 (0.12), residues: 1893 sheet: -2.07 (0.84), residues: 32 loop : 0.23 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 646 HIS 0.004 0.001 HIS A1128 PHE 0.013 0.001 PHE C 64 TYR 0.019 0.001 TYR A1138 ARG 0.007 0.000 ARG E 45 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 1453) hydrogen bonds : angle 3.46011 ( 4236) covalent geometry : bond 0.00246 (22128) covalent geometry : angle 0.49347 (29881) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.8071 (mpt180) cc_final: 0.7839 (mmt-90) REVERT: A 208 GLN cc_start: 0.8887 (tp40) cc_final: 0.8376 (tp40) REVERT: A 426 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8454 (mttm) REVERT: A 533 LEU cc_start: 0.9157 (mp) cc_final: 0.8957 (mm) REVERT: A 546 LYS cc_start: 0.7647 (pptt) cc_final: 0.7446 (pptt) REVERT: B 305 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8097 (tptp) REVERT: B 476 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: B 531 GLU cc_start: 0.8058 (mp0) cc_final: 0.7750 (mp0) REVERT: C 97 MET cc_start: 0.6884 (mmt) cc_final: 0.6491 (tmt) REVERT: C 503 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: E 6 MET cc_start: 0.8004 (tmm) cc_final: 0.7667 (tmm) REVERT: E 36 ASN cc_start: 0.8137 (t0) cc_final: 0.7904 (t0) REVERT: E 77 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7783 (m-30) outliers start: 18 outliers final: 10 residues processed: 202 average time/residue: 1.6821 time to fit residues: 380.6340 Evaluate side-chains 203 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 930 TYR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 503 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 136 optimal weight: 0.0770 chunk 152 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 260 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.084793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.070800 restraints weight = 45192.364| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.82 r_work: 0.3013 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 22128 Z= 0.123 Angle : 0.499 16.356 29881 Z= 0.258 Chirality : 0.037 0.185 3373 Planarity : 0.003 0.047 3811 Dihedral : 3.297 17.726 2922 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.87 % Allowed : 14.71 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.17), residues: 2641 helix: 2.65 (0.12), residues: 1892 sheet: -2.11 (0.84), residues: 32 loop : 0.22 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.005 0.001 HIS C 60 PHE 0.018 0.001 PHE C 64 TYR 0.019 0.001 TYR A1138 ARG 0.007 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 1453) hydrogen bonds : angle 3.46390 ( 4236) covalent geometry : bond 0.00281 (22128) covalent geometry : angle 0.49907 (29881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18947.52 seconds wall clock time: 328 minutes 36.45 seconds (19716.45 seconds total)