Starting phenix.real_space_refine on Tue Jul 23 02:53:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhk_36271/07_2024/8jhk_36271.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhk_36271/07_2024/8jhk_36271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhk_36271/07_2024/8jhk_36271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhk_36271/07_2024/8jhk_36271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhk_36271/07_2024/8jhk_36271.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhk_36271/07_2024/8jhk_36271.cif" } resolution = 4.76 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 116 5.16 5 C 13112 2.51 5 N 3470 2.21 5 O 3814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 317": "OD1" <-> "OD2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 500": "OD1" <-> "OD2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A ARG 522": "NH1" <-> "NH2" Residue "A ASP 527": "OD1" <-> "OD2" Residue "A ARG 531": "NH1" <-> "NH2" Residue "A TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 590": "OD1" <-> "OD2" Residue "A ASP 676": "OD1" <-> "OD2" Residue "A ASP 708": "OD1" <-> "OD2" Residue "A TYR 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 33": "OD1" <-> "OD2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B ASP 338": "OD1" <-> "OD2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B GLU 538": "OE1" <-> "OE2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 558": "OD1" <-> "OD2" Residue "B TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B GLU 599": "OE1" <-> "OE2" Residue "B GLU 687": "OE1" <-> "OE2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 785": "OD1" <-> "OD2" Residue "B ASP 849": "OD1" <-> "OD2" Residue "B PHE 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 891": "OD1" <-> "OD2" Residue "B ASP 892": "OD1" <-> "OD2" Residue "B PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 995": "OD1" <-> "OD2" Residue "B TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1082": "OE1" <-> "OE2" Residue "B GLU 1160": "OE1" <-> "OE2" Residue "B TYR 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1582": "OD1" <-> "OD2" Residue "B PHE 1626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1289": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20512 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5879 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 693} Chain: "B" Number of atoms: 13436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1642, 13436 Classifications: {'peptide': 1642} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1583} Chain: "E" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1197 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Time building chain proxies: 12.07, per 1000 atoms: 0.59 Number of scatterers: 20512 At special positions: 0 Unit cell: (176.89, 135.66, 159.6, 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 116 16.00 O 3814 8.00 N 3470 7.00 C 13112 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: 8.66 Conformation dependent library (CDL) restraints added in 3.9 seconds 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4818 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 14 sheets defined 60.5% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 31 through 41 removed outlier: 3.870A pdb=" N TRP A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.926A pdb=" N ASN A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 124 through 140 removed outlier: 4.003A pdb=" N LEU A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 167 removed outlier: 4.434A pdb=" N ILE A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.756A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 236 through 253 removed outlier: 3.865A pdb=" N LYS A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 270 Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 287 through 310 removed outlier: 4.562A pdb=" N ARG A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 333 Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 366 through 372 removed outlier: 4.351A pdb=" N ASP A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 372 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 391 Processing helix chain 'A' and resid 391 through 402 Processing helix chain 'A' and resid 412 through 429 Processing helix chain 'A' and resid 442 through 446 Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 476 through 494 Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 510 through 521 removed outlier: 3.560A pdb=" N ILE A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 515 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ARG A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 removed outlier: 4.205A pdb=" N SER A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 559 removed outlier: 3.518A pdb=" N LEU A 536 " --> pdb=" O PRO A 532 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A 541 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Proline residue: A 542 - end of helix removed outlier: 4.094A pdb=" N GLU A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 627 removed outlier: 4.180A pdb=" N GLU A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 659 through 672 Processing helix chain 'A' and resid 679 through 698 removed outlier: 4.880A pdb=" N ASP A 687 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N THR A 688 " --> pdb=" O ASN A 684 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 701 No H-bonds generated for 'chain 'A' and resid 699 through 701' Processing helix chain 'B' and resid 8 through 11 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 83 through 104 removed outlier: 4.279A pdb=" N LEU B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 104 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 133 Processing helix chain 'B' and resid 137 through 159 removed outlier: 3.607A pdb=" N LEU B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 207 removed outlier: 3.739A pdb=" N GLN B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 219 removed outlier: 4.311A pdb=" N ILE B 219 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.561A pdb=" N LEU B 588 " --> pdb=" O TYR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 604 Processing helix chain 'B' and resid 634 through 642 removed outlier: 3.584A pdb=" N ASN B 642 " --> pdb=" O LEU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 647 removed outlier: 3.739A pdb=" N ASN B 646 " --> pdb=" O ASN B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 658 removed outlier: 4.324A pdb=" N MET B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 668 removed outlier: 3.518A pdb=" N ILE B 665 " --> pdb=" O ASP B 661 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE B 668 " --> pdb=" O GLU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 683 Processing helix chain 'B' and resid 686 through 705 Processing helix chain 'B' and resid 709 through 711 No H-bonds generated for 'chain 'B' and resid 709 through 711' Processing helix chain 'B' and resid 712 through 724 Processing helix chain 'B' and resid 728 through 743 Processing helix chain 'B' and resid 746 through 758 removed outlier: 4.202A pdb=" N GLU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 779 removed outlier: 3.729A pdb=" N LEU B 763 " --> pdb=" O ALA B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 802 Processing helix chain 'B' and resid 803 through 804 No H-bonds generated for 'chain 'B' and resid 803 through 804' Processing helix chain 'B' and resid 805 through 808 Processing helix chain 'B' and resid 809 through 820 Processing helix chain 'B' and resid 823 through 828 Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'B' and resid 832 through 846 removed outlier: 3.902A pdb=" N SER B 846 " --> pdb=" O LYS B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 866 removed outlier: 3.976A pdb=" N SER B 866 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 891 removed outlier: 4.000A pdb=" N CYS B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU B 876 " --> pdb=" O SER B 872 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) Proline residue: B 880 - end of helix removed outlier: 4.464A pdb=" N ASP B 891 " --> pdb=" O SER B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 915 removed outlier: 4.417A pdb=" N GLU B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 943 removed outlier: 6.743A pdb=" N ARG B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ARG B 935 " --> pdb=" O ARG B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 964 removed outlier: 4.114A pdb=" N PHE B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 972 Processing helix chain 'B' and resid 978 through 998 removed outlier: 3.543A pdb=" N GLY B 998 " --> pdb=" O LYS B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1032 Processing helix chain 'B' and resid 1033 through 1037 Processing helix chain 'B' and resid 1042 through 1055 Processing helix chain 'B' and resid 1058 through 1064 Processing helix chain 'B' and resid 1065 through 1077 Processing helix chain 'B' and resid 1078 through 1095 removed outlier: 4.463A pdb=" N GLU B1082 " --> pdb=" O ASP B1078 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B1095 " --> pdb=" O TRP B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1100 Processing helix chain 'B' and resid 1101 through 1114 removed outlier: 5.261A pdb=" N GLY B1107 " --> pdb=" O PRO B1103 " (cutoff:3.500A) Proline residue: B1108 - end of helix removed outlier: 4.525A pdb=" N GLU B1111 " --> pdb=" O GLY B1107 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B1112 " --> pdb=" O PRO B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1125 Processing helix chain 'B' and resid 1125 through 1138 removed outlier: 3.989A pdb=" N PHE B1129 " --> pdb=" O ILE B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1162 removed outlier: 5.668A pdb=" N GLU B1150 " --> pdb=" O MET B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1181 Processing helix chain 'B' and resid 1185 through 1215 removed outlier: 3.905A pdb=" N MET B1212 " --> pdb=" O ARG B1208 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN B1213 " --> pdb=" O THR B1209 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP B1214 " --> pdb=" O ILE B1210 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU B1215 " --> pdb=" O ILE B1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 1216 through 1234 Processing helix chain 'B' and resid 1236 through 1255 Processing helix chain 'B' and resid 1257 through 1269 Processing helix chain 'B' and resid 1292 through 1311 removed outlier: 3.773A pdb=" N LEU B1296 " --> pdb=" O THR B1292 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1332 Processing helix chain 'B' and resid 1334 through 1355 Processing helix chain 'B' and resid 1373 through 1377 Processing helix chain 'B' and resid 1390 through 1401 Processing helix chain 'B' and resid 1447 through 1457 removed outlier: 3.721A pdb=" N LEU B1451 " --> pdb=" O PRO B1447 " (cutoff:3.500A) Processing helix chain 'B' and resid 1513 through 1537 Processing helix chain 'B' and resid 1544 through 1556 Processing helix chain 'B' and resid 1560 through 1568 removed outlier: 3.733A pdb=" N ASN B1565 " --> pdb=" O GLY B1561 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR B1566 " --> pdb=" O GLY B1562 " (cutoff:3.500A) Processing helix chain 'B' and resid 1573 through 1578 Processing helix chain 'B' and resid 1583 through 1611 removed outlier: 4.170A pdb=" N GLU B1587 " --> pdb=" O GLN B1583 " (cutoff:3.500A) Proline residue: B1598 - end of helix Processing helix chain 'B' and resid 1614 through 1635 removed outlier: 3.996A pdb=" N LEU B1618 " --> pdb=" O GLN B1614 " (cutoff:3.500A) Processing helix chain 'E' and resid 1217 through 1235 Processing helix chain 'E' and resid 1236 through 1255 Processing helix chain 'E' and resid 1257 through 1271 Processing helix chain 'E' and resid 1292 through 1312 Processing helix chain 'E' and resid 1314 through 1331 removed outlier: 3.715A pdb=" N GLU E1323 " --> pdb=" O LYS E1319 " (cutoff:3.500A) Processing helix chain 'E' and resid 1334 through 1354 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'A' and resid 561 through 563 Processing sheet with id=AA4, first strand: chain 'A' and resid 616 through 617 removed outlier: 3.751A pdb=" N ILE A 644 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 232 removed outlier: 3.895A pdb=" N VAL B 401 " --> pdb=" O HIS B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.909A pdb=" N TYR B 246 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER B 295 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET B 327 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 323 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ARG B 302 " --> pdb=" O PRO B 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 279 through 282 removed outlier: 6.823A pdb=" N VAL B 280 " --> pdb=" O ALA B 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 484 through 485 removed outlier: 6.193A pdb=" N ILE B 451 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU B 511 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N THR B 449 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL B 513 " --> pdb=" O TYR B 447 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR B 447 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 515 " --> pdb=" O ASP B 445 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP B 445 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 449 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 451 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLN B 621 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE B 620 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 484 through 485 removed outlier: 6.193A pdb=" N ILE B 451 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU B 511 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N THR B 449 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL B 513 " --> pdb=" O TYR B 447 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR B 447 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 515 " --> pdb=" O ASP B 445 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP B 445 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP B 445 " --> pdb=" O CYS B 627 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 466 through 472 removed outlier: 3.813A pdb=" N ARG B 532 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS B 533 " --> pdb=" O ALA B 546 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA B 546 " --> pdb=" O HIS B 533 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1379 through 1384 removed outlier: 3.681A pdb=" N PHE B1363 " --> pdb=" O TYR B1383 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR B1362 " --> pdb=" O VAL B1431 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B1427 " --> pdb=" O GLY B1366 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1379 through 1384 removed outlier: 3.681A pdb=" N PHE B1363 " --> pdb=" O TYR B1383 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR B1362 " --> pdb=" O VAL B1431 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B1427 " --> pdb=" O GLY B1366 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 3222 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: 7.26 Time building geometry restraints manager: 9.46 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: 6656 1.34 - 1.46: 4501 1.46 - 1.58: 9582 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 20937 Sorted by residual: bond pdb=" CA ASP B 849 " pdb=" C ASP B 849 " ideal model delta sigma weight residual 1.523 1.498 0.026 1.34e-02 5.57e+03 3.67e+00 bond pdb=" C TYR A 18 " pdb=" N PRO A 19 " ideal model delta sigma weight residual 1.333 1.317 0.016 1.01e-02 9.80e+03 2.52e+00 bond pdb=" CB GLN B 885 " pdb=" CG GLN B 885 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.26e+00 bond pdb=" CG PRO A 376 " pdb=" CD PRO A 376 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.23e+00 bond pdb=" CG GLN B 885 " pdb=" CD GLN B 885 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.23e+00 ... (remaining 20932 not shown) Histogram of bond angle deviations from ideal: 97.15 - 104.79: 321 104.79 - 112.43: 10573 112.43 - 120.07: 8565 120.07 - 127.72: 8624 127.72 - 135.36: 164 Bond angle restraints: 28247 Sorted by residual: angle pdb=" C LYS B1423 " pdb=" N GLN B1424 " pdb=" CA GLN B1424 " ideal model delta sigma weight residual 121.26 129.47 -8.21 1.59e+00 3.96e-01 2.67e+01 angle pdb=" N GLN B1424 " pdb=" CA GLN B1424 " pdb=" C GLN B1424 " ideal model delta sigma weight residual 110.30 116.60 -6.30 1.50e+00 4.44e-01 1.76e+01 angle pdb=" N VAL E1279 " pdb=" CA VAL E1279 " pdb=" C VAL E1279 " ideal model delta sigma weight residual 107.76 111.98 -4.22 1.01e+00 9.80e-01 1.74e+01 angle pdb=" CA LEU B 753 " pdb=" CB LEU B 753 " pdb=" CG LEU B 753 " ideal model delta sigma weight residual 116.30 101.97 14.33 3.50e+00 8.16e-02 1.68e+01 angle pdb=" C GLN B1302 " pdb=" N GLU B1303 " pdb=" CA GLU B1303 " ideal model delta sigma weight residual 120.31 114.29 6.02 1.52e+00 4.33e-01 1.57e+01 ... (remaining 28242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 11321 17.80 - 35.61: 1262 35.61 - 53.41: 179 53.41 - 71.21: 43 71.21 - 89.02: 14 Dihedral angle restraints: 12819 sinusoidal: 5394 harmonic: 7425 Sorted by residual: dihedral pdb=" CA SER A 643 " pdb=" C SER A 643 " pdb=" N ILE A 644 " pdb=" CA ILE A 644 " ideal model delta harmonic sigma weight residual 180.00 148.42 31.58 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA PHE B1064 " pdb=" C PHE B1064 " pdb=" N SER B1065 " pdb=" CA SER B1065 " ideal model delta harmonic sigma weight residual 180.00 148.93 31.07 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA TYR B1288 " pdb=" C TYR B1288 " pdb=" N TYR B1289 " pdb=" CA TYR B1289 " ideal model delta harmonic sigma weight residual 180.00 149.59 30.41 0 5.00e+00 4.00e-02 3.70e+01 ... (remaining 12816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2095 0.046 - 0.092: 794 0.092 - 0.138: 189 0.138 - 0.184: 32 0.184 - 0.230: 8 Chirality restraints: 3118 Sorted by residual: chirality pdb=" CA GLU B1458 " pdb=" N GLU B1458 " pdb=" C GLU B1458 " pdb=" CB GLU B1458 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU B1338 " pdb=" CB LEU B1338 " pdb=" CD1 LEU B1338 " pdb=" CD2 LEU B1338 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU B1323 " pdb=" N GLU B1323 " pdb=" C GLU B1323 " pdb=" CB GLU B1323 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3115 not shown) Planarity restraints: 3616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 375 " -0.065 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO A 376 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 376 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 376 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 174 " -0.057 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO B 175 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 175 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 175 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 656 " 0.050 5.00e-02 4.00e+02 7.63e-02 9.31e+00 pdb=" N PRO A 657 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 657 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 657 " 0.042 5.00e-02 4.00e+02 ... (remaining 3613 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 496 2.61 - 3.18: 21868 3.18 - 3.76: 35692 3.76 - 4.33: 49325 4.33 - 4.90: 72389 Nonbonded interactions: 179770 Sorted by model distance: nonbonded pdb=" O GLU A 238 " pdb=" OG1 THR A 241 " model vdw 2.041 2.440 nonbonded pdb=" OE1 GLU B1573 " pdb=" NE2 GLN B1577 " model vdw 2.054 2.520 nonbonded pdb=" O PHE B 216 " pdb=" OH TYR B 222 " model vdw 2.056 2.440 nonbonded pdb=" O ARG B1357 " pdb=" NE2 GLN B1359 " model vdw 2.079 2.520 nonbonded pdb=" O LEU B1059 " pdb=" OG1 THR B1063 " model vdw 2.087 2.440 ... (remaining 179765 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: 1.490 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: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 56.710 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 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 : 0.006 0.055 20937 Z= 0.370 Angle : 0.940 14.329 28247 Z= 0.513 Chirality : 0.051 0.230 3118 Planarity : 0.006 0.100 3616 Dihedral : 14.925 89.016 8001 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 36.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.03 (0.15), residues: 2503 helix: -1.32 (0.13), residues: 1313 sheet: -2.59 (0.33), residues: 193 loop : -2.75 (0.18), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 41 HIS 0.011 0.002 HIS B 154 PHE 0.020 0.002 PHE B 798 TYR 0.027 0.003 TYR A 588 ARG 0.010 0.001 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TRP cc_start: 0.3536 (m-90) cc_final: 0.3256 (m-90) REVERT: A 132 MET cc_start: 0.8163 (ppp) cc_final: 0.7886 (ppp) REVERT: A 290 MET cc_start: 0.7225 (mmp) cc_final: 0.6884 (mmt) REVERT: A 309 MET cc_start: 0.6785 (ppp) cc_final: 0.5908 (ppp) REVERT: A 310 MET cc_start: 0.8584 (mpp) cc_final: 0.8085 (mpp) REVERT: A 369 MET cc_start: 0.6587 (mmp) cc_final: 0.6353 (mmm) REVERT: B 283 ASP cc_start: 0.7035 (m-30) cc_final: 0.6555 (t70) REVERT: B 306 MET cc_start: -0.2201 (mtt) cc_final: -0.2604 (mtt) REVERT: B 680 MET cc_start: 0.8806 (ppp) cc_final: 0.8599 (ppp) REVERT: B 683 MET cc_start: 0.7090 (tmm) cc_final: 0.6713 (tmm) REVERT: B 694 PHE cc_start: 0.9222 (t80) cc_final: 0.8684 (t80) REVERT: B 798 PHE cc_start: 0.9563 (m-80) cc_final: 0.9282 (m-80) REVERT: B 1007 MET cc_start: 0.8175 (ppp) cc_final: 0.7686 (ppp) REVERT: B 1008 VAL cc_start: 0.8881 (t) cc_final: 0.8294 (t) REVERT: B 1011 MET cc_start: 0.8991 (mpp) cc_final: 0.8479 (mpp) REVERT: B 1101 PHE cc_start: 0.8935 (m-80) cc_final: 0.8468 (m-80) REVERT: E 1228 LEU cc_start: 0.9497 (mt) cc_final: 0.9271 (mt) REVERT: E 1240 TYR cc_start: 0.8783 (t80) cc_final: 0.8558 (t80) REVERT: E 1303 GLU cc_start: 0.9524 (mp0) cc_final: 0.9308 (mp0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.3037 time to fit residues: 93.1372 Evaluate side-chains 149 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 9.9990 chunk 189 optimal weight: 0.8980 chunk 105 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 127 optimal weight: 0.4980 chunk 101 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 GLN ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 ASN ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS B1149 ASN B1449 GLN ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20937 Z= 0.228 Angle : 0.727 11.433 28247 Z= 0.380 Chirality : 0.045 0.171 3118 Planarity : 0.006 0.086 3616 Dihedral : 6.702 52.169 2731 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.31 % Allowed : 8.53 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.35 (0.16), residues: 2503 helix: -0.71 (0.13), residues: 1367 sheet: -2.07 (0.33), residues: 207 loop : -2.63 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 41 HIS 0.008 0.001 HIS A 89 PHE 0.015 0.002 PHE B 869 TYR 0.027 0.002 TYR B 969 ARG 0.005 0.001 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 222 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TRP cc_start: 0.3409 (m-90) cc_final: 0.2970 (m-10) REVERT: A 132 MET cc_start: 0.7828 (ppp) cc_final: 0.7601 (ppp) REVERT: A 290 MET cc_start: 0.7279 (mmp) cc_final: 0.6929 (mmt) REVERT: A 309 MET cc_start: 0.6967 (ppp) cc_final: 0.6427 (ppp) REVERT: B 120 MET cc_start: 0.9014 (mmp) cc_final: 0.8797 (mmm) REVERT: B 283 ASP cc_start: 0.7181 (m-30) cc_final: 0.6671 (t70) REVERT: B 306 MET cc_start: -0.2032 (mtt) cc_final: -0.2408 (mtt) REVERT: B 680 MET cc_start: 0.8850 (ppp) cc_final: 0.8631 (ppp) REVERT: B 683 MET cc_start: 0.7020 (tmm) cc_final: 0.6660 (tmm) REVERT: B 694 PHE cc_start: 0.9265 (t80) cc_final: 0.8741 (t80) REVERT: B 787 PHE cc_start: 0.9376 (t80) cc_final: 0.8907 (t80) REVERT: B 798 PHE cc_start: 0.9495 (m-80) cc_final: 0.9183 (m-80) REVERT: B 964 MET cc_start: 0.6800 (ptm) cc_final: 0.6415 (ptm) REVERT: B 1008 VAL cc_start: 0.8948 (t) cc_final: 0.8407 (t) REVERT: B 1101 PHE cc_start: 0.8827 (m-80) cc_final: 0.8380 (m-80) REVERT: B 1201 LEU cc_start: 0.9599 (mm) cc_final: 0.9340 (mm) REVERT: B 1328 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: B 1348 PHE cc_start: 0.8654 (m-10) cc_final: 0.8268 (m-10) REVERT: E 1228 LEU cc_start: 0.9384 (mt) cc_final: 0.9175 (mt) outliers start: 7 outliers final: 3 residues processed: 228 average time/residue: 0.3421 time to fit residues: 124.7956 Evaluate side-chains 168 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 126 optimal weight: 10.0000 chunk 70 optimal weight: 40.0000 chunk 188 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 245 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 HIS ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 GLN ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 ASN ** B1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1535 GLN ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 20937 Z= 0.407 Angle : 0.871 14.778 28247 Z= 0.459 Chirality : 0.049 0.210 3118 Planarity : 0.007 0.087 3616 Dihedral : 7.165 47.355 2731 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 36.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.59 % Favored : 88.37 % Rotamer: Outliers : 0.35 % Allowed : 9.14 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.69 (0.16), residues: 2503 helix: -1.02 (0.13), residues: 1349 sheet: -2.45 (0.31), residues: 227 loop : -2.65 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 173 HIS 0.009 0.002 HIS B 949 PHE 0.019 0.003 PHE B 869 TYR 0.032 0.003 TYR B1328 ARG 0.005 0.001 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TRP cc_start: 0.3279 (m-90) cc_final: 0.2967 (m-10) REVERT: A 208 MET cc_start: 0.8560 (tmm) cc_final: 0.8063 (tmm) REVERT: A 309 MET cc_start: 0.7148 (ppp) cc_final: 0.6663 (ppp) REVERT: A 444 MET cc_start: 0.6971 (ptm) cc_final: 0.6553 (pmm) REVERT: B 283 ASP cc_start: 0.7532 (m-30) cc_final: 0.7100 (t70) REVERT: B 306 MET cc_start: -0.1704 (mtt) cc_final: -0.1927 (mtt) REVERT: B 467 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7404 (mt-10) REVERT: B 680 MET cc_start: 0.8866 (ppp) cc_final: 0.8592 (ppp) REVERT: B 683 MET cc_start: 0.7179 (tmm) cc_final: 0.6954 (tmm) REVERT: B 694 PHE cc_start: 0.9193 (t80) cc_final: 0.8586 (t80) REVERT: B 795 PHE cc_start: 0.9333 (m-10) cc_final: 0.9058 (m-10) REVERT: B 798 PHE cc_start: 0.9522 (m-80) cc_final: 0.9237 (m-80) REVERT: B 860 MET cc_start: 0.8888 (mtp) cc_final: 0.8676 (mtp) REVERT: B 964 MET cc_start: 0.6660 (ptm) cc_final: 0.6400 (ptm) REVERT: B 1007 MET cc_start: 0.8297 (ppp) cc_final: 0.7768 (ppp) REVERT: B 1008 VAL cc_start: 0.9016 (t) cc_final: 0.8317 (t) REVERT: B 1011 MET cc_start: 0.8982 (mpp) cc_final: 0.8349 (mpp) REVERT: B 1101 PHE cc_start: 0.8804 (m-80) cc_final: 0.8449 (m-80) REVERT: B 1303 GLU cc_start: 0.8983 (mp0) cc_final: 0.8754 (mp0) REVERT: E 1228 LEU cc_start: 0.9425 (mt) cc_final: 0.9081 (mt) outliers start: 8 outliers final: 2 residues processed: 188 average time/residue: 0.3074 time to fit residues: 93.7212 Evaluate side-chains 148 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 224 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 118 optimal weight: 0.0870 chunk 25 optimal weight: 0.0570 chunk 108 optimal weight: 0.4980 chunk 152 optimal weight: 0.0270 chunk 228 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 ASN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** B 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 ASN ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1526 ASN ** B1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20937 Z= 0.194 Angle : 0.706 12.476 28247 Z= 0.366 Chirality : 0.044 0.192 3118 Planarity : 0.005 0.085 3616 Dihedral : 6.293 40.490 2731 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.26 % Allowed : 5.20 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.93 (0.16), residues: 2503 helix: -0.37 (0.14), residues: 1359 sheet: -1.99 (0.33), residues: 216 loop : -2.38 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 41 HIS 0.008 0.001 HIS B 154 PHE 0.026 0.002 PHE E1348 TYR 0.026 0.002 TYR B1328 ARG 0.020 0.001 ARG B 534 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 246 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TRP cc_start: 0.3393 (m-90) cc_final: 0.3083 (m-10) REVERT: A 132 MET cc_start: 0.7786 (ppp) cc_final: 0.7553 (ppp) REVERT: A 208 MET cc_start: 0.8665 (tmm) cc_final: 0.8281 (tmm) REVERT: A 309 MET cc_start: 0.6992 (ppp) cc_final: 0.6356 (ppp) REVERT: A 549 LYS cc_start: 0.9473 (pptt) cc_final: 0.9271 (pptt) REVERT: A 692 MET cc_start: 0.8742 (mmp) cc_final: 0.8515 (mmm) REVERT: A 727 ASN cc_start: 0.6505 (t0) cc_final: 0.6298 (t0) REVERT: B 90 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8139 (pm20) REVERT: B 120 MET cc_start: 0.9053 (mmp) cc_final: 0.8735 (mmp) REVERT: B 283 ASP cc_start: 0.7573 (m-30) cc_final: 0.7238 (t70) REVERT: B 306 MET cc_start: -0.2237 (mtt) cc_final: -0.2591 (mtp) REVERT: B 470 MET cc_start: 0.6567 (ppp) cc_final: 0.6319 (ppp) REVERT: B 683 MET cc_start: 0.7087 (tmm) cc_final: 0.6793 (tmm) REVERT: B 694 PHE cc_start: 0.9257 (t80) cc_final: 0.8649 (t80) REVERT: B 787 PHE cc_start: 0.9327 (t80) cc_final: 0.8898 (t80) REVERT: B 798 PHE cc_start: 0.9547 (m-80) cc_final: 0.9154 (m-80) REVERT: B 800 MET cc_start: 0.9140 (tmm) cc_final: 0.8728 (tmm) REVERT: B 943 MET cc_start: 0.8445 (mtp) cc_final: 0.8229 (mtp) REVERT: B 1008 VAL cc_start: 0.9036 (t) cc_final: 0.8508 (t) REVERT: B 1101 PHE cc_start: 0.8686 (m-80) cc_final: 0.8341 (m-80) REVERT: B 1201 LEU cc_start: 0.9561 (mm) cc_final: 0.9234 (mm) REVERT: B 1247 LEU cc_start: 0.9245 (mm) cc_final: 0.9037 (mt) REVERT: B 1265 LEU cc_start: 0.9268 (mp) cc_final: 0.9058 (mp) REVERT: B 1303 GLU cc_start: 0.8969 (mp0) cc_final: 0.8762 (mp0) REVERT: B 1348 PHE cc_start: 0.8577 (m-10) cc_final: 0.8189 (m-10) REVERT: B 1380 ILE cc_start: 0.8653 (mp) cc_final: 0.8347 (mm) REVERT: E 1240 TYR cc_start: 0.8724 (t80) cc_final: 0.8463 (t80) outliers start: 6 outliers final: 2 residues processed: 250 average time/residue: 0.3037 time to fit residues: 121.8220 Evaluate side-chains 177 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 201 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 206 optimal weight: 0.9980 chunk 167 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 216 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 ASN B1213 GLN ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20937 Z= 0.242 Angle : 0.732 13.172 28247 Z= 0.380 Chirality : 0.045 0.219 3118 Planarity : 0.005 0.076 3616 Dihedral : 6.220 35.208 2731 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 26.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.87 (0.16), residues: 2503 helix: -0.37 (0.14), residues: 1358 sheet: -1.62 (0.36), residues: 196 loop : -2.38 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 102 HIS 0.012 0.001 HIS A 89 PHE 0.025 0.002 PHE A 187 TYR 0.023 0.002 TYR B1328 ARG 0.017 0.001 ARG B 534 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7947 (mp0) cc_final: 0.7589 (mp0) REVERT: A 309 MET cc_start: 0.7142 (ppp) cc_final: 0.6510 (ppp) REVERT: A 310 MET cc_start: 0.8447 (mpp) cc_final: 0.8052 (mpp) REVERT: A 678 MET cc_start: 0.8377 (mmm) cc_final: 0.8165 (mmm) REVERT: A 692 MET cc_start: 0.8850 (mmp) cc_final: 0.8592 (mmm) REVERT: B 283 ASP cc_start: 0.7542 (m-30) cc_final: 0.7202 (t70) REVERT: B 306 MET cc_start: -0.1611 (mtt) cc_final: -0.1851 (mtp) REVERT: B 680 MET cc_start: 0.8716 (ppp) cc_final: 0.8495 (ppp) REVERT: B 683 MET cc_start: 0.7108 (tmm) cc_final: 0.6872 (tmm) REVERT: B 694 PHE cc_start: 0.9359 (t80) cc_final: 0.8900 (t80) REVERT: B 785 ASP cc_start: 0.8804 (m-30) cc_final: 0.8578 (p0) REVERT: B 798 PHE cc_start: 0.9468 (m-80) cc_final: 0.9163 (m-80) REVERT: B 800 MET cc_start: 0.9155 (tmm) cc_final: 0.8718 (tmm) REVERT: B 943 MET cc_start: 0.8477 (mtp) cc_final: 0.8115 (mtp) REVERT: B 1033 MET cc_start: 0.9034 (mmm) cc_final: 0.8458 (mmp) REVERT: B 1090 MET cc_start: 0.8595 (tpt) cc_final: 0.8305 (mtp) REVERT: B 1101 PHE cc_start: 0.8682 (m-80) cc_final: 0.8338 (m-80) REVERT: B 1265 LEU cc_start: 0.9324 (mp) cc_final: 0.9106 (mp) REVERT: B 1348 PHE cc_start: 0.8672 (m-10) cc_final: 0.8263 (m-10) REVERT: B 1380 ILE cc_start: 0.8775 (mp) cc_final: 0.8554 (mm) REVERT: E 1228 LEU cc_start: 0.9368 (mt) cc_final: 0.9109 (mt) REVERT: E 1231 TYR cc_start: 0.8957 (m-80) cc_final: 0.8718 (m-80) REVERT: E 1240 TYR cc_start: 0.8740 (t80) cc_final: 0.8337 (t80) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.2859 time to fit residues: 101.0305 Evaluate side-chains 156 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 81 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 241 optimal weight: 1.9990 chunk 200 optimal weight: 0.2980 chunk 111 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 126 optimal weight: 20.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 HIS ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 ASN B1213 GLN ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20937 Z= 0.239 Angle : 0.724 12.554 28247 Z= 0.376 Chirality : 0.045 0.233 3118 Planarity : 0.005 0.079 3616 Dihedral : 6.147 29.338 2731 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 26.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.81 (0.16), residues: 2503 helix: -0.30 (0.14), residues: 1353 sheet: -1.69 (0.36), residues: 189 loop : -2.35 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 41 HIS 0.011 0.001 HIS A 89 PHE 0.031 0.002 PHE E1348 TYR 0.021 0.002 TYR E1231 ARG 0.013 0.000 ARG B 534 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7937 (mp0) cc_final: 0.7573 (mp0) REVERT: A 132 MET cc_start: 0.7629 (ppp) cc_final: 0.7272 (ppp) REVERT: A 309 MET cc_start: 0.6780 (ppp) cc_final: 0.6163 (ppp) REVERT: A 692 MET cc_start: 0.8824 (mmp) cc_final: 0.8600 (mmm) REVERT: B 694 PHE cc_start: 0.9347 (t80) cc_final: 0.8880 (t80) REVERT: B 785 ASP cc_start: 0.8814 (m-30) cc_final: 0.8560 (p0) REVERT: B 798 PHE cc_start: 0.9490 (m-80) cc_final: 0.9170 (m-80) REVERT: B 943 MET cc_start: 0.8477 (mtp) cc_final: 0.8095 (mtp) REVERT: B 1101 PHE cc_start: 0.8664 (m-80) cc_final: 0.8365 (m-80) REVERT: B 1265 LEU cc_start: 0.9344 (mp) cc_final: 0.9103 (mp) REVERT: B 1303 GLU cc_start: 0.8902 (mp0) cc_final: 0.8650 (mp0) REVERT: B 1348 PHE cc_start: 0.8661 (m-10) cc_final: 0.8250 (m-10) REVERT: B 1380 ILE cc_start: 0.8778 (mp) cc_final: 0.8546 (mm) REVERT: E 1228 LEU cc_start: 0.9385 (mt) cc_final: 0.9124 (mt) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.2893 time to fit residues: 103.6068 Evaluate side-chains 164 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 233 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 240 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 146 optimal weight: 0.5980 chunk 111 optimal weight: 8.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1066 GLN B1149 ASN B1203 ASN B1213 GLN ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20937 Z= 0.237 Angle : 0.735 12.223 28247 Z= 0.379 Chirality : 0.045 0.178 3118 Planarity : 0.005 0.078 3616 Dihedral : 6.100 29.282 2731 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 26.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.78 (0.16), residues: 2503 helix: -0.29 (0.14), residues: 1350 sheet: -1.69 (0.36), residues: 197 loop : -2.31 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 41 HIS 0.011 0.001 HIS A 89 PHE 0.015 0.002 PHE B1372 TYR 0.026 0.002 TYR E1231 ARG 0.011 0.000 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7936 (mp0) cc_final: 0.7567 (mp0) REVERT: A 132 MET cc_start: 0.7695 (ppp) cc_final: 0.7418 (ppp) REVERT: A 208 MET cc_start: 0.8496 (tmm) cc_final: 0.8079 (tmm) REVERT: A 309 MET cc_start: 0.6730 (ppp) cc_final: 0.6086 (ppp) REVERT: A 692 MET cc_start: 0.8817 (mmp) cc_final: 0.8590 (mmm) REVERT: B 694 PHE cc_start: 0.9311 (t80) cc_final: 0.8887 (t80) REVERT: B 785 ASP cc_start: 0.8783 (m-30) cc_final: 0.8549 (p0) REVERT: B 798 PHE cc_start: 0.9477 (m-80) cc_final: 0.9163 (m-80) REVERT: B 933 LEU cc_start: 0.8871 (mt) cc_final: 0.8641 (mt) REVERT: B 1060 GLN cc_start: 0.8176 (pp30) cc_final: 0.7953 (pp30) REVERT: B 1090 MET cc_start: 0.8587 (tpt) cc_final: 0.8360 (mtp) REVERT: B 1101 PHE cc_start: 0.8636 (m-80) cc_final: 0.8315 (m-80) REVERT: B 1348 PHE cc_start: 0.8663 (m-10) cc_final: 0.8254 (m-10) REVERT: B 1380 ILE cc_start: 0.8739 (mp) cc_final: 0.8508 (mm) REVERT: E 1228 LEU cc_start: 0.9399 (mt) cc_final: 0.9185 (mt) REVERT: E 1238 ASP cc_start: 0.9234 (p0) cc_final: 0.8961 (p0) REVERT: E 1258 THR cc_start: 0.8185 (p) cc_final: 0.7459 (p) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2952 time to fit residues: 108.6501 Evaluate side-chains 166 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 149 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 HIS B1149 ASN B1213 GLN ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1267 HIS ** E1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20937 Z= 0.256 Angle : 0.759 12.508 28247 Z= 0.393 Chirality : 0.046 0.192 3118 Planarity : 0.005 0.076 3616 Dihedral : 6.132 28.216 2731 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 26.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.78 (0.16), residues: 2503 helix: -0.33 (0.14), residues: 1346 sheet: -1.68 (0.37), residues: 193 loop : -2.24 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 41 HIS 0.010 0.001 HIS A 89 PHE 0.033 0.002 PHE E1348 TYR 0.025 0.002 TYR E1231 ARG 0.010 0.001 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7915 (mp0) cc_final: 0.7582 (mp0) REVERT: A 132 MET cc_start: 0.7814 (ppp) cc_final: 0.7501 (ppp) REVERT: A 208 MET cc_start: 0.8511 (tmm) cc_final: 0.8099 (tmm) REVERT: A 309 MET cc_start: 0.6937 (ppp) cc_final: 0.6203 (ppp) REVERT: A 310 MET cc_start: 0.8323 (mpp) cc_final: 0.7797 (mpp) REVERT: A 678 MET cc_start: 0.8304 (mmp) cc_final: 0.8079 (mmm) REVERT: B 689 TYR cc_start: 0.8355 (m-80) cc_final: 0.8116 (m-80) REVERT: B 694 PHE cc_start: 0.9299 (t80) cc_final: 0.8887 (t80) REVERT: B 785 ASP cc_start: 0.8784 (m-30) cc_final: 0.8553 (p0) REVERT: B 798 PHE cc_start: 0.9474 (m-80) cc_final: 0.9187 (m-80) REVERT: B 943 MET cc_start: 0.8288 (mtp) cc_final: 0.8084 (mtp) REVERT: B 1101 PHE cc_start: 0.8665 (m-80) cc_final: 0.8276 (m-80) REVERT: B 1348 PHE cc_start: 0.8672 (m-10) cc_final: 0.8266 (m-10) REVERT: B 1380 ILE cc_start: 0.8788 (mp) cc_final: 0.8560 (mm) REVERT: E 1228 LEU cc_start: 0.9395 (mt) cc_final: 0.9183 (mt) REVERT: E 1238 ASP cc_start: 0.9246 (p0) cc_final: 0.8721 (p0) REVERT: E 1303 GLU cc_start: 0.9521 (mp0) cc_final: 0.9308 (mp0) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2956 time to fit residues: 105.3562 Evaluate side-chains 164 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 219 optimal weight: 0.4980 chunk 230 optimal weight: 10.0000 chunk 210 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN A 268 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 HIS B1149 ASN B1213 GLN ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1267 HIS ** E1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20937 Z= 0.249 Angle : 0.765 12.326 28247 Z= 0.397 Chirality : 0.047 0.278 3118 Planarity : 0.005 0.076 3616 Dihedral : 6.120 29.159 2731 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 26.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.78 (0.16), residues: 2503 helix: -0.36 (0.14), residues: 1343 sheet: -1.51 (0.37), residues: 202 loop : -2.21 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 41 HIS 0.008 0.001 HIS A 89 PHE 0.014 0.002 PHE B1372 TYR 0.024 0.002 TYR E1231 ARG 0.009 0.001 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7901 (mp0) cc_final: 0.7569 (mp0) REVERT: A 208 MET cc_start: 0.8511 (tmm) cc_final: 0.8094 (tmm) REVERT: A 290 MET cc_start: 0.7206 (mmp) cc_final: 0.7003 (mmt) REVERT: A 309 MET cc_start: 0.7168 (ppp) cc_final: 0.6413 (ppp) REVERT: A 310 MET cc_start: 0.8472 (mpp) cc_final: 0.7972 (mpp) REVERT: A 678 MET cc_start: 0.8357 (mmp) cc_final: 0.8117 (mmm) REVERT: B 158 MET cc_start: 0.8689 (mtp) cc_final: 0.8478 (mtp) REVERT: B 680 MET cc_start: 0.8627 (ppp) cc_final: 0.8426 (ppp) REVERT: B 689 TYR cc_start: 0.8354 (m-80) cc_final: 0.8118 (m-80) REVERT: B 694 PHE cc_start: 0.9283 (t80) cc_final: 0.8880 (t80) REVERT: B 785 ASP cc_start: 0.8778 (m-30) cc_final: 0.8550 (p0) REVERT: B 798 PHE cc_start: 0.9467 (m-80) cc_final: 0.9180 (m-80) REVERT: B 980 GLN cc_start: 0.8674 (mp10) cc_final: 0.8409 (tm-30) REVERT: B 1090 MET cc_start: 0.8614 (tpt) cc_final: 0.8303 (mtp) REVERT: B 1101 PHE cc_start: 0.8655 (m-80) cc_final: 0.8270 (m-80) REVERT: B 1348 PHE cc_start: 0.8669 (m-10) cc_final: 0.8259 (m-10) REVERT: B 1380 ILE cc_start: 0.8759 (mp) cc_final: 0.8519 (mm) REVERT: E 1228 LEU cc_start: 0.9408 (mt) cc_final: 0.9200 (mt) REVERT: E 1238 ASP cc_start: 0.9047 (p0) cc_final: 0.8348 (p0) REVERT: E 1303 GLU cc_start: 0.9512 (mp0) cc_final: 0.9285 (mp0) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2916 time to fit residues: 104.6339 Evaluate side-chains 162 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 147 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 165 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN A 268 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 HIS B1149 ASN B1203 ASN B1213 GLN ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20937 Z= 0.237 Angle : 0.760 12.032 28247 Z= 0.393 Chirality : 0.046 0.264 3118 Planarity : 0.005 0.078 3616 Dihedral : 6.076 29.916 2731 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 25.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.78 (0.16), residues: 2503 helix: -0.34 (0.14), residues: 1343 sheet: -1.73 (0.36), residues: 203 loop : -2.19 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 41 HIS 0.008 0.001 HIS A 89 PHE 0.037 0.002 PHE E1348 TYR 0.023 0.002 TYR E1231 ARG 0.009 0.001 ARG B 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7898 (mp0) cc_final: 0.7557 (mp0) REVERT: A 41 TRP cc_start: 0.3607 (m-90) cc_final: 0.3326 (m-90) REVERT: A 132 MET cc_start: 0.7560 (ppp) cc_final: 0.7317 (ppp) REVERT: A 309 MET cc_start: 0.7189 (ppp) cc_final: 0.6385 (ppp) REVERT: A 310 MET cc_start: 0.8485 (mpp) cc_final: 0.7999 (mpp) REVERT: A 678 MET cc_start: 0.8378 (mmp) cc_final: 0.8150 (mmm) REVERT: B 306 MET cc_start: -0.0890 (mtt) cc_final: -0.1107 (mtt) REVERT: B 680 MET cc_start: 0.8636 (ppp) cc_final: 0.8430 (ppp) REVERT: B 689 TYR cc_start: 0.8356 (m-80) cc_final: 0.8144 (m-80) REVERT: B 694 PHE cc_start: 0.9268 (t80) cc_final: 0.8869 (t80) REVERT: B 722 LYS cc_start: 0.8908 (mmpt) cc_final: 0.8526 (pttp) REVERT: B 785 ASP cc_start: 0.8768 (m-30) cc_final: 0.8542 (p0) REVERT: B 798 PHE cc_start: 0.9458 (m-80) cc_final: 0.9163 (m-80) REVERT: B 800 MET cc_start: 0.9156 (tmm) cc_final: 0.8945 (tmm) REVERT: B 943 MET cc_start: 0.8230 (mtp) cc_final: 0.7880 (mtp) REVERT: B 1101 PHE cc_start: 0.8653 (m-80) cc_final: 0.8267 (m-80) REVERT: B 1348 PHE cc_start: 0.8668 (m-10) cc_final: 0.8251 (m-10) REVERT: E 1303 GLU cc_start: 0.9524 (mp0) cc_final: 0.9304 (mp0) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2835 time to fit residues: 101.6389 Evaluate side-chains 163 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 157 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 182 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 198 optimal weight: 0.9990 chunk 83 optimal weight: 0.0570 chunk 203 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1022 ASN B1293 GLN ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1267 HIS ** E1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.062023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.038934 restraints weight = 144500.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.040548 restraints weight = 87254.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.041649 restraints weight = 61506.620| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20937 Z= 0.188 Angle : 0.723 11.286 28247 Z= 0.373 Chirality : 0.045 0.251 3118 Planarity : 0.005 0.072 3616 Dihedral : 5.672 31.320 2731 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.47 (0.17), residues: 2503 helix: -0.11 (0.14), residues: 1356 sheet: -1.31 (0.37), residues: 205 loop : -2.12 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 41 HIS 0.010 0.001 HIS A 89 PHE 0.010 0.001 PHE B1138 TYR 0.055 0.002 TYR E1328 ARG 0.009 0.001 ARG B 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3656.14 seconds wall clock time: 67 minutes 32.41 seconds (4052.41 seconds total)