Starting phenix.real_space_refine on Wed Nov 20 13:47:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usc_26732/11_2024/7usc_26732.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usc_26732/11_2024/7usc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usc_26732/11_2024/7usc_26732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usc_26732/11_2024/7usc_26732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usc_26732/11_2024/7usc_26732.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usc_26732/11_2024/7usc_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 13.10, per 1000 atoms: 0.60 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: 6.07 Conformation dependent library (CDL) restraints added in 2.8 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: 2.31 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: 7.46 Time building geometry restraints manager: 6.99 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: 1.120 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: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 48.970 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.690 ------------------------------------------------------------------------------- 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= 0.445 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 *********************** 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 : 2.811 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: 1.8016 time to fit residues: 578.5157 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 : 2.600 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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= 0.365 Angle : 0.569 10.006 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 *********************** 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 : 2.528 Fit side-chains REVERT: A 150 LYS cc_start: 0.8775 (pptt) cc_final: 0.8564 (ptmm) REVERT: A 208 GLN cc_start: 0.8356 (tp40) cc_final: 0.7849 (tp40) REVERT: A 533 LEU cc_start: 0.8954 (mp) cc_final: 0.8735 (mm) REVERT: B 392 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.6203 (pmm) REVERT: B 601 MET cc_start: 0.8190 (tmm) cc_final: 0.7986 (ttp) REVERT: D 49 THR cc_start: 0.9155 (m) cc_final: 0.8781 (p) REVERT: D 53 LYS cc_start: 0.8862 (tptt) cc_final: 0.8662 (mmmm) REVERT: E 6 MET cc_start: 0.7356 (tmm) cc_final: 0.7077 (tmm) REVERT: E 74 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7798 (mp10) outliers start: 33 outliers final: 10 residues processed: 219 average time/residue: 1.6693 time to fit residues: 409.3339 Evaluate side-chains 207 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 2.692 ------------------------------------------------------------------------------- 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 134 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 241 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 194 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 107 GLN C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22128 Z= 0.339 Angle : 0.545 16.519 29881 Z= 0.289 Chirality : 0.041 0.252 3373 Planarity : 0.004 0.046 3811 Dihedral : 3.792 21.036 2922 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.65 % Allowed : 9.23 % Favored : 89.12 % 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: 2.18 (0.17), residues: 2641 helix: 2.15 (0.12), residues: 1871 sheet: -2.51 (0.87), residues: 32 loop : -0.18 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.006 0.001 HIS A1128 PHE 0.024 0.001 PHE B 549 TYR 0.022 0.001 TYR A1138 ARG 0.005 0.000 ARG B 547 *********************** 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 244 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 2.578 Fit side-chains REVERT: A 150 LYS cc_start: 0.8774 (pptt) cc_final: 0.8569 (ptmm) REVERT: A 208 GLN cc_start: 0.8378 (tp40) cc_final: 0.7842 (tp40) REVERT: A 533 LEU cc_start: 0.8975 (mp) cc_final: 0.8752 (mm) REVERT: B 305 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.8022 (tptt) REVERT: B 392 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6197 (pmm) REVERT: D 49 THR cc_start: 0.9154 (m) cc_final: 0.8774 (p) REVERT: E 36 ASN cc_start: 0.8548 (t0) cc_final: 0.8293 (t0) REVERT: E 74 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7793 (mp10) outliers start: 40 outliers final: 12 residues processed: 218 average time/residue: 1.6738 time to fit residues: 408.9490 Evaluate side-chains 209 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 2.638 ------------------------------------------------------------------------------- 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 A residue 740 LEU Chi-restraints excluded: chain B residue 49 ILE 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 930 TYR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain E residue 33 CYS Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 94 SER 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 239 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 242 optimal weight: 6.9990 chunk 257 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22128 Z= 0.174 Angle : 0.482 16.591 29881 Z= 0.255 Chirality : 0.037 0.188 3373 Planarity : 0.003 0.048 3811 Dihedral : 3.583 19.385 2922 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.36 % Allowed : 11.00 % Favored : 87.64 % 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: 2.56 (0.17), residues: 2641 helix: 2.43 (0.12), residues: 1876 sheet: -2.29 (0.86), residues: 32 loop : -0.02 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.004 0.001 HIS A1128 PHE 0.016 0.001 PHE B 549 TYR 0.019 0.001 TYR A1138 ARG 0.006 0.000 ARG B 547 *********************** 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 240 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 2.595 Fit side-chains REVERT: A 208 GLN cc_start: 0.8306 (tp40) cc_final: 0.7887 (tp40) REVERT: A 533 LEU cc_start: 0.8967 (mp) cc_final: 0.8750 (mm) REVERT: B 305 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7907 (tptp) REVERT: E 36 ASN cc_start: 0.8550 (t0) cc_final: 0.8306 (t0) outliers start: 33 outliers final: 8 residues processed: 218 average time/residue: 1.6684 time to fit residues: 407.3485 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 : 2.628 ------------------------------------------------------------------------------- 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 248 MET Chi-restraints excluded: chain B residue 305 LYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 191 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 131 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 74 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22128 Z= 0.245 Angle : 0.503 16.714 29881 Z= 0.263 Chirality : 0.038 0.189 3373 Planarity : 0.003 0.048 3811 Dihedral : 3.536 19.686 2922 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.11 % Allowed : 12.36 % Favored : 86.53 % 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: 2.62 (0.17), residues: 2641 helix: 2.46 (0.12), residues: 1876 sheet: -2.27 (0.87), residues: 32 loop : 0.04 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.006 0.001 HIS A1128 PHE 0.015 0.001 PHE B 549 TYR 0.025 0.001 TYR C 156 ARG 0.006 0.000 ARG B 547 *********************** 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 227 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8290 (tp40) cc_final: 0.7913 (tp40) REVERT: A 533 LEU cc_start: 0.8980 (mp) cc_final: 0.8760 (mm) REVERT: B 297 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8539 (ptp-170) REVERT: B 305 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7972 (tptt) REVERT: E 36 ASN cc_start: 0.8572 (t0) cc_final: 0.8317 (t0) outliers start: 27 outliers final: 13 residues processed: 214 average time/residue: 1.7124 time to fit residues: 415.7335 Evaluate side-chains 212 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 2.752 ------------------------------------------------------------------------------- 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 1038 LYS Chi-restraints excluded: chain B residue 49 ILE 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 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 86 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 257 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22128 Z= 0.286 Angle : 0.516 16.993 29881 Z= 0.269 Chirality : 0.039 0.189 3373 Planarity : 0.004 0.047 3811 Dihedral : 3.552 20.180 2922 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.07 % Allowed : 13.14 % Favored : 85.78 % 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: 2.59 (0.17), residues: 2641 helix: 2.42 (0.12), residues: 1881 sheet: -2.25 (0.88), residues: 32 loop : 0.06 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.006 0.001 HIS A1128 PHE 0.015 0.001 PHE B1002 TYR 0.026 0.001 TYR C 156 ARG 0.006 0.000 ARG B 547 *********************** 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 229 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 2.693 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8281 (tp40) cc_final: 0.7898 (tp40) REVERT: A 533 LEU cc_start: 0.8987 (mp) cc_final: 0.8767 (mm) REVERT: B 305 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8012 (tptt) REVERT: D 38 SER cc_start: 0.8843 (m) cc_final: 0.8455 (p) REVERT: E 36 ASN cc_start: 0.8557 (t0) cc_final: 0.8296 (t0) outliers start: 26 outliers final: 12 residues processed: 217 average time/residue: 1.6504 time to fit residues: 402.9951 Evaluate side-chains 213 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 88 SER 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 1038 LYS Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 LYS 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 94 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 143 optimal weight: 0.6980 chunk 256 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22128 Z= 0.184 Angle : 0.487 17.034 29881 Z= 0.255 Chirality : 0.037 0.185 3373 Planarity : 0.003 0.048 3811 Dihedral : 3.469 18.740 2922 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.11 % Allowed : 13.93 % Favored : 84.96 % 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: 2.75 (0.17), residues: 2641 helix: 2.54 (0.12), residues: 1879 sheet: -2.14 (0.90), residues: 32 loop : 0.10 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 646 HIS 0.005 0.001 HIS A1128 PHE 0.013 0.001 PHE A 391 TYR 0.027 0.001 TYR C 156 ARG 0.008 0.000 ARG B 763 *********************** 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 232 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 2.727 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8245 (tp40) cc_final: 0.7881 (tp40) REVERT: A 533 LEU cc_start: 0.8983 (mp) cc_final: 0.8763 (mm) REVERT: B 305 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7931 (tptp) REVERT: D 38 SER cc_start: 0.8847 (m) cc_final: 0.8437 (p) REVERT: E 36 ASN cc_start: 0.8560 (t0) cc_final: 0.8310 (t0) outliers start: 27 outliers final: 13 residues processed: 220 average time/residue: 1.6231 time to fit residues: 401.4590 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 : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 164 PHE 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 211 GLN Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 LYS 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 77 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22128 Z= 0.301 Angle : 0.528 17.305 29881 Z= 0.275 Chirality : 0.039 0.189 3373 Planarity : 0.004 0.047 3811 Dihedral : 3.518 19.811 2922 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.95 % Allowed : 14.75 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.17), residues: 2641 helix: 2.43 (0.12), residues: 1882 sheet: -2.24 (0.89), residues: 32 loop : 0.09 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.006 0.001 HIS A1128 PHE 0.015 0.001 PHE A 391 TYR 0.029 0.001 TYR C 156 ARG 0.007 0.000 ARG E 45 *********************** 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 221 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 2.804 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8243 (tp40) cc_final: 0.7956 (tp40) REVERT: A 533 LEU cc_start: 0.8998 (mp) cc_final: 0.8778 (mm) REVERT: B 305 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8025 (tptt) REVERT: D 38 SER cc_start: 0.8841 (m) cc_final: 0.8424 (p) REVERT: E 36 ASN cc_start: 0.8550 (t0) cc_final: 0.8271 (t0) outliers start: 23 outliers final: 14 residues processed: 212 average time/residue: 1.7126 time to fit residues: 407.2146 Evaluate side-chains 212 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 164 PHE 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 211 GLN Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 305 LYS 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 77 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 224 optimal weight: 0.0470 chunk 238 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 187 optimal weight: 0.3980 chunk 73 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 225 optimal weight: 0.7980 chunk 156 optimal weight: 8.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN C 109 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 22128 Z= 0.154 Angle : 0.499 17.437 29881 Z= 0.260 Chirality : 0.037 0.185 3373 Planarity : 0.003 0.048 3811 Dihedral : 3.413 18.021 2922 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.70 % Allowed : 15.08 % Favored : 84.22 % 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: 2.56 (0.12), residues: 1894 sheet: -2.09 (0.90), residues: 32 loop : 0.17 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 646 HIS 0.004 0.001 HIS A1128 PHE 0.011 0.001 PHE A 391 TYR 0.019 0.001 TYR A1138 ARG 0.006 0.000 ARG E 45 *********************** 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: 17 poor density : 200 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8207 (tp40) cc_final: 0.7968 (tp40) REVERT: A 533 LEU cc_start: 0.8989 (mp) cc_final: 0.8781 (mm) REVERT: D 38 SER cc_start: 0.8828 (m) cc_final: 0.8400 (p) REVERT: E 36 ASN cc_start: 0.8528 (t0) cc_final: 0.8284 (t0) outliers start: 17 outliers final: 11 residues processed: 210 average time/residue: 1.6004 time to fit residues: 377.4375 Evaluate side-chains 202 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 248 MET 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 48 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 175 optimal weight: 0.5980 chunk 265 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: