Starting phenix.real_space_refine on Mon Dec 11 21:56:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr0_23952/12_2023/7mr0_23952.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr0_23952/12_2023/7mr0_23952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr0_23952/12_2023/7mr0_23952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr0_23952/12_2023/7mr0_23952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr0_23952/12_2023/7mr0_23952.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr0_23952/12_2023/7mr0_23952.pdb" } resolution = 3.7 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= 0.000 sd= 0.004 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 89 5.16 5 C 12214 2.51 5 N 3378 2.21 5 O 3601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 575": "OE1" <-> "OE2" Residue "B GLU 629": "OE1" <-> "OE2" Residue "B GLU 672": "OE1" <-> "OE2" Residue "B GLU 1020": "OE1" <-> "OE2" Residue "B GLU 1054": "OE1" <-> "OE2" Residue "B GLU 1149": "OE1" <-> "OE2" Residue "C GLU 273": "OE1" <-> "OE2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C GLU 543": "OE1" <-> "OE2" Residue "C GLU 648": "OE1" <-> "OE2" Residue "C GLU 942": "OE1" <-> "OE2" Residue "C GLU 983": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 19282 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 9247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1156, 9247 Classifications: {'peptide': 1156} Link IDs: {'PTRANS': 52, 'TRANS': 1103} Chain breaks: 1 Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Time building chain proxies: 10.55, per 1000 atoms: 0.55 Number of scatterers: 19282 At special positions: 0 Unit cell: (150.29, 127.69, 141.25, 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 89 16.00 O 3601 8.00 N 3378 7.00 C 12214 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 - 3.50 Amino acid : False - 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: 7.19 Conformation dependent library (CDL) restraints added in 3.9 seconds 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 17 sheets defined 56.0% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.612A pdb=" N ALA B 49 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.640A pdb=" N GLU B 58 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 59' Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 128 through 140 removed outlier: 3.715A pdb=" N ARG B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.188A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 5.702A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 240 removed outlier: 3.979A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 Processing helix chain 'B' and resid 275 through 281 removed outlier: 3.914A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 279 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR B 280 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN B 281 " --> pdb=" O ASN B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 275 through 281' Processing helix chain 'B' and resid 282 through 288 Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.970A pdb=" N ASP B 314 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.352A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 366 through 378 removed outlier: 3.887A pdb=" N LEU B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.524A pdb=" N GLN B 417 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 414 through 418' Processing helix chain 'B' and resid 427 through 437 Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.664A pdb=" N ASN B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 534 Processing helix chain 'B' and resid 560 through 574 Processing helix chain 'B' and resid 586 through 589 removed outlier: 3.920A pdb=" N GLU B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 589' Processing helix chain 'B' and resid 590 through 605 removed outlier: 4.294A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 Processing helix chain 'B' and resid 624 through 634 removed outlier: 3.714A pdb=" N ASP B 634 " --> pdb=" O THR B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 656 Processing helix chain 'B' and resid 657 through 669 Processing helix chain 'B' and resid 669 through 677 Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.803A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 717 Processing helix chain 'B' and resid 742 through 745 removed outlier: 3.627A pdb=" N LYS B 745 " --> pdb=" O HIS B 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 742 through 745' Processing helix chain 'B' and resid 783 through 808 removed outlier: 3.664A pdb=" N VAL B 787 " --> pdb=" O ALA B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 835 Processing helix chain 'B' and resid 836 through 843 removed outlier: 3.669A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.846A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 941 through 945 Processing helix chain 'B' and resid 949 through 959 removed outlier: 4.184A pdb=" N PHE B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 980 Processing helix chain 'B' and resid 983 through 985 No H-bonds generated for 'chain 'B' and resid 983 through 985' Processing helix chain 'B' and resid 986 through 998 removed outlier: 3.739A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR B 995 " --> pdb=" O THR B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 Processing helix chain 'B' and resid 1013 through 1015 No H-bonds generated for 'chain 'B' and resid 1013 through 1015' Processing helix chain 'B' and resid 1032 through 1041 removed outlier: 3.591A pdb=" N ASP B1037 " --> pdb=" O ALA B1033 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1049 removed outlier: 4.188A pdb=" N GLY B1049 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1094 removed outlier: 4.110A pdb=" N THR B1094 " --> pdb=" O SER B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1106 Processing helix chain 'B' and resid 1107 through 1126 removed outlier: 4.069A pdb=" N TYR B1111 " --> pdb=" O TYR B1107 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN B1112 " --> pdb=" O ASP B1108 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS B1124 " --> pdb=" O ARG B1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1135 Processing helix chain 'B' and resid 1163 through 1173 removed outlier: 3.812A pdb=" N GLU B1170 " --> pdb=" O ALA B1166 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.216A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.711A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 121 through 142 Processing helix chain 'C' and resid 143 through 152 removed outlier: 3.911A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 180 Proline residue: C 167 - end of helix removed outlier: 3.770A pdb=" N GLY C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 removed outlier: 4.106A pdb=" N TYR C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 Processing helix chain 'C' and resid 255 through 260 Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 315 Processing helix chain 'C' and resid 333 through 345 Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.657A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 418 through 429 Processing helix chain 'C' and resid 430 through 434 removed outlier: 3.744A pdb=" N TYR C 434 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 459 Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 removed outlier: 4.053A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 501 removed outlier: 4.378A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY C 501 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 513 Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 538 through 542 removed outlier: 3.631A pdb=" N GLN C 541 " --> pdb=" O GLU C 538 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY C 542 " --> pdb=" O SER C 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 538 through 542' Processing helix chain 'C' and resid 557 through 578 removed outlier: 4.309A pdb=" N VAL C 561 " --> pdb=" O ILE C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 589 through 599 Processing helix chain 'C' and resid 604 through 626 removed outlier: 4.330A pdb=" N ALA C 608 " --> pdb=" O GLU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 645 removed outlier: 3.922A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN C 643 " --> pdb=" O ASP C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 removed outlier: 3.597A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 790 through 795 removed outlier: 4.071A pdb=" N TYR C 794 " --> pdb=" O ASP C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 806 through 811 Processing helix chain 'C' and resid 833 through 843 removed outlier: 4.243A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 852 Processing helix chain 'C' and resid 873 through 889 Processing helix chain 'C' and resid 893 through 904 removed outlier: 4.049A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 933 removed outlier: 3.832A pdb=" N GLN C 926 " --> pdb=" O GLN C 922 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 990 Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.871A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1050 Processing helix chain 'C' and resid 1060 through 1076 Processing helix chain 'C' and resid 1087 through 1094 Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1120 Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 32 through 48 Processing helix chain 'D' and resid 54 through 61 Processing helix chain 'D' and resid 66 through 72 Processing helix chain 'D' and resid 80 through 88 removed outlier: 4.020A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 124 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 5.775A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 411 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 126 through 127 removed outlier: 5.798A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 60 " --> pdb=" O MET B 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.779A pdb=" N GLN B 151 " --> pdb=" O LEU B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.272A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 768 " --> pdb=" O VAL B 777 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'B' and resid 490 through 491 removed outlier: 3.627A pdb=" N VAL B 490 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 539 " --> pdb=" O VAL B 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.603A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 737 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP B 753 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 752 " --> pdb=" O HIS B 812 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER B 814 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 815 " --> pdb=" O LYS B 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 901 through 904 removed outlier: 3.658A pdb=" N MET B1061 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR B 904 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B1058 " --> pdb=" O GLU B1029 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU B1029 " --> pdb=" O VAL B1058 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1017 through 1022 removed outlier: 7.209A pdb=" N ASP B1067 " --> pdb=" O GLU B1020 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU B1022 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE B1065 " --> pdb=" O GLU B1022 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1079 through 1080 removed outlier: 6.494A pdb=" N ASP B1080 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 60 through 61 removed outlier: 4.727A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N THR C 241 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 7 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU C 2 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU C 323 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL C 4 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG C 265 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN C 264 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.369A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 437 through 439 removed outlier: 6.456A pdb=" N ALA C 438 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N THR C 663 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 678 " --> pdb=" O MET C 411 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LYS C 673 " --> pdb=" O GLN C 724 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL C 675 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR C 375 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 729 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR C 731 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 442 through 443 removed outlier: 4.243A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE C 650 " --> pdb=" O ARG C 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 942 through 947 removed outlier: 3.526A pdb=" N LEU C 945 " --> pdb=" O ILE C 952 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 963 through 967 removed outlier: 5.636A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 100 through 102 900 hydrogen bonds defined for protein. 2655 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: 7.83 Time building geometry restraints manager: 7.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6534 1.34 - 1.46: 4311 1.46 - 1.58: 8730 1.58 - 1.70: 1 1.70 - 1.82: 149 Bond restraints: 19725 Sorted by residual: bond pdb=" C CYS B1050 " pdb=" N PRO B1051 " ideal model delta sigma weight residual 1.329 1.385 -0.056 1.18e-02 7.18e+03 2.23e+01 bond pdb=" CA MET B 121 " pdb=" C MET B 121 " ideal model delta sigma weight residual 1.522 1.576 -0.054 1.41e-02 5.03e+03 1.46e+01 bond pdb=" C LEU C 460 " pdb=" N PRO C 461 " ideal model delta sigma weight residual 1.337 1.378 -0.042 1.11e-02 8.12e+03 1.40e+01 bond pdb=" C HIS C 448 " pdb=" N PRO C 449 " ideal model delta sigma weight residual 1.335 1.381 -0.046 1.30e-02 5.92e+03 1.23e+01 bond pdb=" CA CYS B1050 " pdb=" C CYS B1050 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.00e-02 1.00e+04 4.76e+00 ... (remaining 19720 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.06: 528 106.06 - 113.09: 10250 113.09 - 120.12: 7317 120.12 - 127.16: 8410 127.16 - 134.19: 279 Bond angle restraints: 26784 Sorted by residual: angle pdb=" N GLY B1137 " pdb=" CA GLY B1137 " pdb=" C GLY B1137 " ideal model delta sigma weight residual 110.97 119.40 -8.43 1.42e+00 4.96e-01 3.52e+01 angle pdb=" CA SER B 619 " pdb=" C SER B 619 " pdb=" N MET B 620 " ideal model delta sigma weight residual 118.08 125.53 -7.45 1.30e+00 5.92e-01 3.28e+01 angle pdb=" N ILE B1139 " pdb=" CA ILE B1139 " pdb=" C ILE B1139 " ideal model delta sigma weight residual 107.37 114.61 -7.24 1.48e+00 4.57e-01 2.39e+01 angle pdb=" N GLU B1054 " pdb=" CA GLU B1054 " pdb=" C GLU B1054 " ideal model delta sigma weight residual 113.02 107.27 5.75 1.20e+00 6.94e-01 2.29e+01 angle pdb=" C ILE B 229 " pdb=" N ASP B 230 " pdb=" CA ASP B 230 " ideal model delta sigma weight residual 121.58 112.95 8.63 1.95e+00 2.63e-01 1.96e+01 ... (remaining 26779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10556 17.99 - 35.98: 1078 35.98 - 53.97: 219 53.97 - 71.96: 35 71.96 - 89.94: 24 Dihedral angle restraints: 11912 sinusoidal: 4906 harmonic: 7006 Sorted by residual: dihedral pdb=" CA LEU B 581 " pdb=" C LEU B 581 " pdb=" N SER B 582 " pdb=" CA SER B 582 " ideal model delta harmonic sigma weight residual 180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA VAL C 889 " pdb=" C VAL C 889 " pdb=" N GLU C 890 " pdb=" CA GLU C 890 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA PRO B 405 " pdb=" C PRO B 405 " pdb=" N GLU B 406 " pdb=" CA GLU B 406 " ideal model delta harmonic sigma weight residual 180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 11909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2460 0.063 - 0.126: 412 0.126 - 0.189: 40 0.189 - 0.252: 3 0.252 - 0.315: 1 Chirality restraints: 2916 Sorted by residual: chirality pdb=" CB THR B 605 " pdb=" CA THR B 605 " pdb=" OG1 THR B 605 " pdb=" CG2 THR B 605 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA GLU C 79 " pdb=" N GLU C 79 " pdb=" C GLU C 79 " pdb=" CB GLU C 79 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE D 75 " pdb=" CA ILE D 75 " pdb=" CG1 ILE D 75 " pdb=" CG2 ILE D 75 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.55e-01 ... (remaining 2913 not shown) Planarity restraints: 3530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 253 " 0.081 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO C 254 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO C 254 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO C 254 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 310 " 0.022 2.00e-02 2.50e+03 2.55e-02 1.13e+01 pdb=" CG PHE B 310 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE B 310 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 310 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE B 310 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 310 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 310 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO C 658 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.041 5.00e-02 4.00e+02 ... (remaining 3527 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4888 2.81 - 3.33: 17346 3.33 - 3.85: 29917 3.85 - 4.38: 32042 4.38 - 4.90: 56878 Nonbonded interactions: 141071 Sorted by model distance: nonbonded pdb=" O LEU C 276 " pdb=" OG SER C 280 " model vdw 2.284 2.440 nonbonded pdb=" O SER B 462 " pdb=" OG SER B 462 " model vdw 2.287 2.440 nonbonded pdb=" O ALA D 90 " pdb=" OG1 THR D 98 " model vdw 2.290 2.440 nonbonded pdb=" OG SER B1090 " pdb=" OE1 GLN B1153 " model vdw 2.295 2.440 nonbonded pdb=" OH TYR B 161 " pdb=" OE1 GLN B 191 " model vdw 2.319 2.440 ... (remaining 141066 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 4.350 Check model and map are aligned: 0.310 Set scattering table: 0.170 Process input model: 54.640 Find NCS groups from input model: 0.700 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.003 0.079 19725 Z= 0.223 Angle : 0.810 12.471 26784 Z= 0.443 Chirality : 0.047 0.315 2916 Planarity : 0.006 0.122 3530 Dihedral : 15.125 89.944 7368 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 0.44 % Allowed : 0.53 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % 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: -1.82 (0.16), residues: 2392 helix: -0.16 (0.14), residues: 1207 sheet: -1.60 (0.38), residues: 189 loop : -2.45 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B1085 HIS 0.008 0.001 HIS B 689 PHE 0.059 0.001 PHE B 310 TYR 0.025 0.001 TYR C 190 ARG 0.014 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 157 time to evaluate : 2.241 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 162 average time/residue: 0.2681 time to fit residues: 71.8297 Evaluate side-chains 121 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 2.308 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1665 time to fit residues: 3.6483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 201 optimal weight: 0.0070 chunk 181 optimal weight: 0.0770 chunk 100 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 122 optimal weight: 0.3980 chunk 96 optimal weight: 9.9990 chunk 187 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 HIS B 742 HIS B 943 HIS B 944 GLN C 757 GLN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19725 Z= 0.124 Angle : 0.521 8.472 26784 Z= 0.262 Chirality : 0.038 0.144 2916 Planarity : 0.005 0.074 3530 Dihedral : 4.368 23.541 2641 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.34 % Allowed : 6.56 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % 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: -0.96 (0.17), residues: 2392 helix: 0.74 (0.15), residues: 1221 sheet: -1.56 (0.36), residues: 196 loop : -2.28 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 574 HIS 0.008 0.001 HIS C1018 PHE 0.016 0.001 PHE B1055 TYR 0.022 0.001 TYR C1075 ARG 0.007 0.000 ARG B 728 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 2.374 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 139 average time/residue: 0.2803 time to fit residues: 65.0144 Evaluate side-chains 125 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 2.240 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1661 time to fit residues: 4.7670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 180 optimal weight: 0.0170 chunk 147 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 217 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 HIS B 222 HIS B 404 GLN B 910 GLN B1003 ASN ** B1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 510 ASN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 19725 Z= 0.436 Angle : 0.717 13.349 26784 Z= 0.364 Chirality : 0.045 0.148 2916 Planarity : 0.005 0.059 3530 Dihedral : 4.913 25.768 2641 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.02 % Favored : 92.93 % Rotamer: Outliers : 1.02 % Allowed : 10.64 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % 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: -1.06 (0.17), residues: 2392 helix: 0.66 (0.15), residues: 1221 sheet: -1.68 (0.37), residues: 193 loop : -2.32 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 901 HIS 0.009 0.002 HIS C 377 PHE 0.033 0.002 PHE B 127 TYR 0.024 0.002 TYR C 728 ARG 0.008 0.001 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 132 average time/residue: 0.2837 time to fit residues: 63.2268 Evaluate side-chains 125 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 2.117 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1776 time to fit residues: 6.3668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 214 optimal weight: 0.0070 chunk 163 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 146 optimal weight: 0.0870 chunk 218 optimal weight: 7.9990 chunk 231 optimal weight: 20.0000 chunk 114 optimal weight: 0.5980 chunk 206 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 overall best weight: 0.9378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1003 ASN ** B1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 GLN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19725 Z= 0.149 Angle : 0.537 10.196 26784 Z= 0.269 Chirality : 0.039 0.143 2916 Planarity : 0.004 0.053 3530 Dihedral : 4.489 24.079 2641 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.53 % Allowed : 12.24 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % 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: -0.63 (0.18), residues: 2392 helix: 1.14 (0.15), residues: 1213 sheet: -1.68 (0.35), residues: 203 loop : -2.20 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 616 HIS 0.005 0.001 HIS B 307 PHE 0.014 0.001 PHE B 127 TYR 0.017 0.001 TYR C1027 ARG 0.007 0.000 ARG B 728 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 2.125 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 133 average time/residue: 0.2582 time to fit residues: 57.9609 Evaluate side-chains 120 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 2.149 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1826 time to fit residues: 4.1547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 192 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 834 HIS B 910 GLN B1003 ASN B1072 HIS ** B1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 757 GLN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 19725 Z= 0.434 Angle : 0.716 14.245 26784 Z= 0.361 Chirality : 0.044 0.152 2916 Planarity : 0.005 0.051 3530 Dihedral : 5.003 25.243 2641 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 1.55 % Allowed : 13.60 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % 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: -1.07 (0.17), residues: 2392 helix: 0.74 (0.15), residues: 1220 sheet: -1.95 (0.35), residues: 200 loop : -2.38 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 901 HIS 0.007 0.002 HIS C1018 PHE 0.023 0.002 PHE B 127 TYR 0.020 0.002 TYR C 728 ARG 0.010 0.001 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 118 time to evaluate : 2.375 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 21 residues processed: 142 average time/residue: 0.2702 time to fit residues: 64.9356 Evaluate side-chains 135 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 2.311 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1806 time to fit residues: 10.1991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 77 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 HIS B 834 HIS ** B1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 757 GLN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19725 Z= 0.282 Angle : 0.613 11.932 26784 Z= 0.309 Chirality : 0.041 0.140 2916 Planarity : 0.005 0.050 3530 Dihedral : 4.832 27.019 2641 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.07 % Allowed : 14.96 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % 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: -0.94 (0.17), residues: 2392 helix: 0.87 (0.15), residues: 1223 sheet: -1.87 (0.36), residues: 196 loop : -2.35 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 981 HIS 0.004 0.001 HIS B 689 PHE 0.018 0.001 PHE C1119 TYR 0.020 0.001 TYR C1027 ARG 0.007 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 2.324 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 136 average time/residue: 0.2756 time to fit residues: 63.3040 Evaluate side-chains 122 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 2.192 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1948 time to fit residues: 5.8613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 222 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 230 optimal weight: 20.0000 chunk 144 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 834 HIS ** B1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 GLN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19725 Z= 0.167 Angle : 0.553 11.259 26784 Z= 0.276 Chirality : 0.040 0.136 2916 Planarity : 0.004 0.051 3530 Dihedral : 4.514 25.245 2641 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.53 % Allowed : 16.37 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % 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: -0.58 (0.18), residues: 2392 helix: 1.23 (0.15), residues: 1207 sheet: -1.83 (0.35), residues: 203 loop : -2.20 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 981 HIS 0.007 0.001 HIS C1018 PHE 0.015 0.001 PHE C 789 TYR 0.019 0.001 TYR C1027 ARG 0.006 0.000 ARG B 728 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 2.413 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 125 average time/residue: 0.2750 time to fit residues: 58.8209 Evaluate side-chains 120 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 2.464 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1886 time to fit residues: 5.0372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 142 optimal weight: 0.0970 chunk 91 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 146 optimal weight: 0.1980 chunk 156 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 910 GLN ** B1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 GLN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19725 Z= 0.143 Angle : 0.526 10.459 26784 Z= 0.261 Chirality : 0.039 0.137 2916 Planarity : 0.004 0.052 3530 Dihedral : 4.199 24.552 2641 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.53 % Allowed : 16.71 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % 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: -0.33 (0.18), residues: 2392 helix: 1.43 (0.15), residues: 1214 sheet: -1.77 (0.35), residues: 193 loop : -2.09 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 981 HIS 0.011 0.001 HIS C1018 PHE 0.014 0.001 PHE B1055 TYR 0.021 0.001 TYR C1027 ARG 0.004 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 2.462 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 131 average time/residue: 0.2730 time to fit residues: 60.4859 Evaluate side-chains 121 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 2.566 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4696 time to fit residues: 5.9893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 209 optimal weight: 4.9990 chunk 220 optimal weight: 0.8980 chunk 201 optimal weight: 0.0010 chunk 214 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 168 optimal weight: 0.0070 chunk 65 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 213 optimal weight: 0.9990 overall best weight: 1.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 GLN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19725 Z= 0.178 Angle : 0.544 11.146 26784 Z= 0.269 Chirality : 0.039 0.168 2916 Planarity : 0.004 0.052 3530 Dihedral : 4.197 22.926 2641 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.53 % Allowed : 16.80 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % 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: -0.29 (0.18), residues: 2392 helix: 1.44 (0.15), residues: 1218 sheet: -1.60 (0.36), residues: 203 loop : -2.07 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 236 HIS 0.005 0.001 HIS B 307 PHE 0.014 0.001 PHE B1055 TYR 0.018 0.001 TYR C1027 ARG 0.004 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 125 average time/residue: 0.2740 time to fit residues: 58.2965 Evaluate side-chains 122 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 2.290 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1870 time to fit residues: 5.4325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 140 optimal weight: 6.9990 chunk 226 optimal weight: 0.4980 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 910 GLN ** B1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 GLN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19725 Z= 0.166 Angle : 0.546 11.675 26784 Z= 0.271 Chirality : 0.039 0.184 2916 Planarity : 0.004 0.051 3530 Dihedral : 4.179 23.390 2641 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.39 % Allowed : 16.61 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % 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: -0.27 (0.18), residues: 2392 helix: 1.47 (0.15), residues: 1219 sheet: -1.71 (0.35), residues: 193 loop : -2.06 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 616 HIS 0.010 0.001 HIS C1018 PHE 0.031 0.001 PHE C1117 TYR 0.018 0.001 TYR C1027 ARG 0.005 0.000 ARG B 728 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 123 average time/residue: 0.2776 time to fit residues: 57.3024 Evaluate side-chains 119 residues out of total 2059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 2.302 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1855 time to fit residues: 4.1350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 150 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 GLN C 850 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.100165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.078300 restraints weight = 51221.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.077623 restraints weight = 34635.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.078326 restraints weight = 27479.042| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19725 Z= 0.287 Angle : 0.617 11.558 26784 Z= 0.308 Chirality : 0.041 0.171 2916 Planarity : 0.004 0.049 3530 Dihedral : 4.486 24.005 2641 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.39 % Allowed : 16.85 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % 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: -0.46 (0.18), residues: 2392 helix: 1.27 (0.15), residues: 1220 sheet: -1.71 (0.36), residues: 205 loop : -2.12 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 901 HIS 0.005 0.001 HIS B 689 PHE 0.016 0.001 PHE C1117 TYR 0.016 0.001 TYR C1027 ARG 0.006 0.000 ARG B 728 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2920.93 seconds wall clock time: 54 minutes 26.15 seconds (3266.15 seconds total)