Starting phenix.real_space_refine (version: dev) on Thu Dec 22 05:44:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyd_8138/12_2022/5iyd_8138.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyd_8138/12_2022/5iyd_8138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyd_8138/12_2022/5iyd_8138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyd_8138/12_2022/5iyd_8138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyd_8138/12_2022/5iyd_8138.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyd_8138/12_2022/5iyd_8138.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 834": "NH1" <-> "NH2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B ARG 885": "NH1" <-> "NH2" Residue "B ARG 897": "NH1" <-> "NH2" Residue "B ARG 1085": "NH1" <-> "NH2" Residue "B GLU 1090": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "G ARG 16": "NH1" <-> "NH2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "L TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "M ARG 28": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 53": "NH1" <-> "NH2" Residue "M ARG 104": "NH1" <-> "NH2" Residue "M ARG 105": "NH1" <-> "NH2" Residue "M ARG 112": "NH1" <-> "NH2" Residue "M ARG 127": "NH1" <-> "NH2" Residue "M ARG 132": "NH1" <-> "NH2" Residue "M TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 248": "NH1" <-> "NH2" Residue "M ARG 290": "NH1" <-> "NH2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N GLU 317": "OE1" <-> "OE2" Residue "N ARG 363": "NH1" <-> "NH2" Residue "O ARG 51": "NH1" <-> "NH2" Residue "O ARG 53": "NH1" <-> "NH2" Residue "P ARG 203": "NH1" <-> "NH2" Residue "P ARG 208": "NH1" <-> "NH2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P ARG 269": "NH1" <-> "NH2" Residue "P ARG 294": "NH1" <-> "NH2" Residue "P ARG 318": "NH1" <-> "NH2" Residue "P ARG 336": "NH1" <-> "NH2" Residue "Q ARG 174": "NH1" <-> "NH2" Residue "Q ARG 179": "NH1" <-> "NH2" Residue "Q ARG 192": "NH1" <-> "NH2" Residue "R GLU 230": "OE1" <-> "OE2" Residue "S GLU 136": "OE1" <-> "OE2" Residue "T GLU 107": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 46709 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 11515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1454, 11515 Classifications: {'peptide': 1454} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1384} Chain breaks: 1 Chain: "B" Number of atoms: 9317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 9317 Classifications: {'peptide': 1165} Link IDs: {'PTRANS': 53, 'TRANS': 1111} Chain: "C" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2213 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "D" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1062 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1723 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Chain: "F" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 689 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1205 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "I" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1013 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 937 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2391 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 16, 'TRANS': 293} Chain: "N" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "O" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "P" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1462 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain: "Q" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1484 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain breaks: 1 Chain: "R" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1357 Classifications: {'peptide': 165} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 158} Chain: "S" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "T" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "X" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1645 Classifications: {'DNA': 80} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 79} Chain: "Y" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1624 Classifications: {'DNA': 80} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 79} Chain: "Z" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 2, ' ZN': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 51.734 120.671 104.038 1.00 0.00 S ATOM 776 SG CYS A 111 99.025 119.103 114.506 1.00 0.00 S ATOM 20539 SG CYS B1137 61.053 129.692 112.408 1.00 0.00 S ATOM 29208 SG CYS I 17 128.543 90.465 64.717 1.00 0.00 S Time building chain proxies: 24.97, per 1000 atoms: 0.53 Number of scatterers: 46709 At special positions: 0 Unit cell: (179.47, 217.46, 170.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 11 29.99 S 255 16.00 P 163 15.00 Mg 2 11.99 O 9148 8.00 N 8194 7.00 C 28936 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: 18.81 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 71 " pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 91 " 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10204 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 53 sheets defined 40.9% alpha, 19.3% beta 57 base pairs and 112 stacking pairs defined. Time for finding SS restraints: 14.11 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 136 through 152 removed outlier: 3.726A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN A 152 " --> pdb=" O CYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.658A pdb=" N ASN A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.710A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.089A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 486 through 490 removed outlier: 4.192A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 518 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 538 through 550 removed outlier: 3.746A pdb=" N LYS A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 567 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.757A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 619 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.644A pdb=" N THR A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.720A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 removed outlier: 3.540A pdb=" N LEU A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.603A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.656A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 937 through 942 removed outlier: 3.628A pdb=" N LYS A 940 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.624A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.526A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 4.817A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 removed outlier: 3.549A pdb=" N ILE A1080 " --> pdb=" O PHE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1144 through 1150 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 3.601A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1180 through 1184 Processing helix chain 'A' and resid 1186 through 1188 No H-bonds generated for 'chain 'A' and resid 1186 through 1188' Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 3.666A pdb=" N VAL A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1206 removed outlier: 4.007A pdb=" N ALA A1205 " --> pdb=" O PHE A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1264 through 1268 removed outlier: 3.809A pdb=" N ASN A1267 " --> pdb=" O SER A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1295 Processing helix chain 'A' and resid 1342 through 1348 removed outlier: 3.960A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 3.998A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.947A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 removed outlier: 3.974A pdb=" N ASN A1420 " --> pdb=" O ARG A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1435 through 1446 Processing helix chain 'A' and resid 1453 through 1461 removed outlier: 3.734A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1476 through 1484 Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.859A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 4.011A pdb=" N LEU B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 60 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 162 through 166 removed outlier: 4.240A pdb=" N GLY B 165 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 309 Proline residue: B 303 - end of helix removed outlier: 3.520A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'B' and resid 332 through 346 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 378 removed outlier: 3.643A pdb=" N LYS B 361 " --> pdb=" O CYS B 357 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.629A pdb=" N ALA B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 435' Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.567A pdb=" N LYS B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 removed outlier: 3.636A pdb=" N THR B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 549 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 579 through 593 Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 636 through 646 removed outlier: 3.827A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.538A pdb=" N GLU B 671 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.506A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 732 removed outlier: 3.571A pdb=" N ASN B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 4.386A pdb=" N HIS B 741 " --> pdb=" O THR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 768 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 844 through 848 removed outlier: 4.250A pdb=" N LYS B 847 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.612A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.217A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1019 removed outlier: 4.011A pdb=" N LYS B1010 " --> pdb=" O VAL B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1059 removed outlier: 3.972A pdb=" N LYS B1058 " --> pdb=" O MET B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1107 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.539A pdb=" N ARG C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 69 Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.609A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 removed outlier: 3.835A pdb=" N LEU C 211 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 269 removed outlier: 3.842A pdb=" N ILE C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.561A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 52 removed outlier: 3.705A pdb=" N GLU D 52 " --> pdb=" O ASN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.638A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 121 removed outlier: 4.099A pdb=" N GLY D 120 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 2 through 25 removed outlier: 4.369A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.589A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 53 through 58 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 122 removed outlier: 3.547A pdb=" N ALA E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.629A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 74 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.599A pdb=" N GLY J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.786A pdb=" N HIS J 52 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.082A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.629A pdb=" N ALA K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 52 removed outlier: 3.695A pdb=" N GLU M 51 " --> pdb=" O ASP M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 110 No H-bonds generated for 'chain 'M' and resid 108 through 110' Processing helix chain 'M' and resid 111 through 128 Processing helix chain 'M' and resid 131 through 149 removed outlier: 3.510A pdb=" N VAL M 135 " --> pdb=" O PRO M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 171 Processing helix chain 'M' and resid 176 through 184 Processing helix chain 'M' and resid 187 through 202 Processing helix chain 'M' and resid 211 through 222 removed outlier: 4.278A pdb=" N SER M 216 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG M 217 " --> pdb=" O ASP M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 242 Processing helix chain 'M' and resid 249 through 264 Processing helix chain 'M' and resid 270 through 279 Processing helix chain 'M' and resid 281 through 293 Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.665A pdb=" N LEU M 299 " --> pdb=" O ARG M 295 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE M 300 " --> pdb=" O ALA M 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 295 through 300' Processing helix chain 'M' and resid 309 through 313 Processing helix chain 'N' and resid 10 through 33 removed outlier: 4.298A pdb=" N ASP N 27 " --> pdb=" O ASN N 23 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE N 28 " --> pdb=" O ASP N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 51 removed outlier: 3.632A pdb=" N LEU N 39 " --> pdb=" O ASP N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 318 removed outlier: 3.575A pdb=" N SER N 316 " --> pdb=" O PRO N 313 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 8 removed outlier: 4.060A pdb=" N TYR O 6 " --> pdb=" O TYR O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 25 Processing helix chain 'O' and resid 29 through 51 Processing helix chain 'P' and resid 153 through 157 Processing helix chain 'P' and resid 179 through 187 Processing helix chain 'P' and resid 205 through 208 Processing helix chain 'P' and resid 226 through 243 Processing helix chain 'P' and resid 269 through 277 removed outlier: 3.661A pdb=" N LEU P 273 " --> pdb=" O ARG P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 335 removed outlier: 3.941A pdb=" N ILE P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Proline residue: P 330 - end of helix Processing helix chain 'Q' and resid 12 through 26 Processing helix chain 'Q' and resid 27 through 39 removed outlier: 4.203A pdb=" N ILE Q 36 " --> pdb=" O LEU Q 32 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Q 37 " --> pdb=" O ALA Q 33 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG Q 39 " --> pdb=" O ASP Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 53 Processing helix chain 'Q' and resid 55 through 69 Processing helix chain 'Q' and resid 102 through 119 removed outlier: 3.728A pdb=" N ASP Q 117 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 144 removed outlier: 3.561A pdb=" N ALA Q 141 " --> pdb=" O THR Q 137 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN Q 142 " --> pdb=" O ASP Q 138 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 188 Proline residue: Q 186 - end of helix Processing helix chain 'Q' and resid 188 through 202 Processing helix chain 'R' and resid 76 through 92 Processing helix chain 'R' and resid 98 through 106 Processing helix chain 'R' and resid 112 through 122 Processing helix chain 'R' and resid 122 through 127 removed outlier: 3.669A pdb=" N ASN R 127 " --> pdb=" O ALA R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 156 Processing helix chain 'R' and resid 167 through 174 removed outlier: 3.867A pdb=" N ALA R 174 " --> pdb=" O ASP R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 185 removed outlier: 4.443A pdb=" N LYS R 180 " --> pdb=" O PRO R 176 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 223 removed outlier: 3.625A pdb=" N ARG R 221 " --> pdb=" O GLN R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 239 Processing helix chain 'S' and resid 34 through 36 No H-bonds generated for 'chain 'S' and resid 34 through 36' Processing helix chain 'S' and resid 38 through 42 Processing helix chain 'S' and resid 160 through 167 Processing helix chain 'S' and resid 173 through 180 removed outlier: 3.934A pdb=" N MET S 177 " --> pdb=" O HIS S 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 15 Processing helix chain 'T' and resid 25 through 33 Processing helix chain 'T' and resid 123 through 136 removed outlier: 4.109A pdb=" N LEU T 127 " --> pdb=" O ASN T 123 " (cutoff:3.500A) Processing helix chain 'T' and resid 158 through 169 Processing helix chain 'T' and resid 179 through 194 removed outlier: 3.604A pdb=" N VAL T 183 " --> pdb=" O ASP T 179 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS T 193 " --> pdb=" O SER T 189 " (cutoff:3.500A) Processing helix chain 'T' and resid 199 through 207 Processing helix chain 'T' and resid 209 through 221 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.913A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 95 removed outlier: 10.742A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 11.127A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 335 removed outlier: 3.746A pdb=" N ARG A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 358 through 359 removed outlier: 3.686A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.792A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.395A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG H 57 " --> pdb=" O LYS H 146 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.606A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.804A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 901 through 905 Processing sheet with id=AB4, first strand: chain 'A' and resid 1309 through 1313 removed outlier: 3.541A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.245A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1320 through 1322 Processing sheet with id=AB7, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.651A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.651A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N ALA G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.875A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC2, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC3, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.383A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.910A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG B 255 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC6, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC7, first strand: chain 'B' and resid 551 through 552 removed outlier: 3.527A pdb=" N GLU B 551 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 576 " --> pdb=" O GLU B 551 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.972A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.972A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD2, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 4.198A pdb=" N GLN B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL B 794 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N TYR B 949 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N MET B 796 " --> pdb=" O TYR B 949 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 965 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 826 through 829 Processing sheet with id=AD4, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AD5, first strand: chain 'B' and resid 1114 through 1119 Processing sheet with id=AD6, first strand: chain 'C' and resid 8 through 14 removed outlier: 7.246A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.775A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AD9, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.634A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE2, first strand: chain 'E' and resid 147 through 150 removed outlier: 5.440A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 56 through 57 removed outlier: 3.907A pdb=" N MET F 57 " --> pdb=" O ILE F 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'G' and resid 84 through 93 removed outlier: 7.372A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 117 through 120 Processing sheet with id=AE6, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE7, first strand: chain 'I' and resid 80 through 81 removed outlier: 3.522A pdb=" N ALA I 94 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'M' and resid 24 through 26 Processing sheet with id=AF1, first strand: chain 'P' and resid 291 through 295 removed outlier: 3.832A pdb=" N GLY P 314 " --> pdb=" O MET P 258 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N MET P 258 " --> pdb=" O GLY P 314 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL P 169 " --> pdb=" O GLN P 256 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N MET P 258 " --> pdb=" O ASN P 167 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN P 167 " --> pdb=" O MET P 258 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY P 260 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU P 165 " --> pdb=" O GLY P 260 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR P 209 " --> pdb=" O ILE P 204 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE P 204 " --> pdb=" O THR P 209 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ALA P 190 " --> pdb=" O ASN O 63 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR O 65 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N TYR P 192 " --> pdb=" O TYR O 65 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N PHE O 67 " --> pdb=" O TYR P 192 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL O 56 " --> pdb=" O GLU O 83 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU O 83 " --> pdb=" O VAL O 56 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE O 58 " --> pdb=" O PHE O 81 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE O 81 " --> pdb=" O PHE O 58 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY O 60 " --> pdb=" O VAL O 79 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL O 79 " --> pdb=" O GLY O 60 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU O 62 " --> pdb=" O ASN O 77 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN O 77 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP O 91 " --> pdb=" O ASP O 78 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLU O 80 " --> pdb=" O LYS O 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS O 89 " --> pdb=" O GLU O 80 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG O 82 " --> pdb=" O LEU O 87 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU O 87 " --> pdb=" O ARG O 82 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN N 333 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS O 94 " --> pdb=" O ASN N 333 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR N 339 " --> pdb=" O CYS O 98 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN N 333 " --> pdb=" O LEU N 360 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU N 360 " --> pdb=" O ASN N 333 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL N 335 " --> pdb=" O MET N 358 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N MET N 358 " --> pdb=" O VAL N 335 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS N 337 " --> pdb=" O GLY N 356 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY N 356 " --> pdb=" O CYS N 337 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR N 339 " --> pdb=" O LYS N 354 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LYS N 354 " --> pdb=" O TYR N 339 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER N 368 " --> pdb=" O ASP N 355 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE N 357 " --> pdb=" O ILE N 366 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE N 366 " --> pdb=" O ILE N 357 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN N 359 " --> pdb=" O ASP N 364 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP N 364 " --> pdb=" O ASN N 359 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL O 56 " --> pdb=" O PHE N 367 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS N 369 " --> pdb=" O VAL O 56 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N PHE O 58 " --> pdb=" O LYS N 369 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE N 371 " --> pdb=" O PHE O 58 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N GLY O 60 " --> pdb=" O ILE N 371 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP N 373 " --> pdb=" O GLY O 60 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU O 62 " --> pdb=" O ASP N 373 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU N 375 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR O 64 " --> pdb=" O GLU N 375 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 72 through 76 Processing sheet with id=AF3, first strand: chain 'Q' and resid 145 through 146 Processing sheet with id=AF4, first strand: chain 'R' and resid 131 through 133 removed outlier: 3.630A pdb=" N GLU R 131 " --> pdb=" O ALA R 138 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 165 through 166 removed outlier: 3.684A pdb=" N GLY R 165 " --> pdb=" O PHE R 202 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE R 202 " --> pdb=" O GLY R 165 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 45 through 49 removed outlier: 4.465A pdb=" N LYS S 109 " --> pdb=" O LEU S 149 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N ASN S 142 " --> pdb=" O LYS S 24 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYR S 26 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N TYR S 144 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE S 28 " --> pdb=" O TYR S 144 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE S 146 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA S 30 " --> pdb=" O PHE S 146 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N ASN S 32 " --> pdb=" O PRO S 148 " (cutoff:3.500A) removed outlier: 11.260A pdb=" N GLN T 91 " --> pdb=" O GLN T 112 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N GLN T 112 " --> pdb=" O GLN T 91 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU T 93 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR T 97 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU T 106 " --> pdb=" O THR T 97 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER T 99 " --> pdb=" O LEU T 104 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU T 104 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL T 18 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN T 112 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N GLY T 17 " --> pdb=" O GLN S 129 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLN S 129 " --> pdb=" O GLY T 17 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR S 125 " --> pdb=" O VAL T 21 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL T 23 " --> pdb=" O SER S 123 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE S 135 " --> pdb=" O GLU S 13 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL S 15 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA S 137 " --> pdb=" O VAL S 15 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG S 17 " --> pdb=" O ALA S 137 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY T 41 " --> pdb=" O VAL S 16 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 45 through 49 removed outlier: 4.465A pdb=" N LYS S 109 " --> pdb=" O LEU S 149 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N ASN S 142 " --> pdb=" O LYS S 24 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYR S 26 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N TYR S 144 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE S 28 " --> pdb=" O TYR S 144 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE S 146 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA S 30 " --> pdb=" O PHE S 146 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N ASN S 32 " --> pdb=" O PRO S 148 " (cutoff:3.500A) removed outlier: 11.260A pdb=" N GLN T 91 " --> pdb=" O GLN T 112 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N GLN T 112 " --> pdb=" O GLN T 91 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU T 93 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR T 97 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU T 106 " --> pdb=" O THR T 97 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER T 99 " --> pdb=" O LEU T 104 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU T 104 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASP T 8 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY T 108 " --> pdb=" O ASP T 8 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 197 through 198 removed outlier: 3.516A pdb=" N TYR T 197 " --> pdb=" O TRP T 233 " (cutoff:3.500A) 1920 hydrogen bonds defined for protein. 5331 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 147 hydrogen bonds 282 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 112 stacking parallelities Total time for adding SS restraints: 30.84 Time building geometry restraints manager: 20.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8936 1.32 - 1.46: 16022 1.46 - 1.60: 22307 1.60 - 1.74: 241 1.74 - 1.88: 401 Bond restraints: 47907 Sorted by residual: bond pdb=" CA HIS B 939 " pdb=" C HIS B 939 " ideal model delta sigma weight residual 1.526 1.444 0.082 1.23e-02 6.61e+03 4.41e+01 bond pdb=" CA ASN A1291 " pdb=" CB ASN A1291 " ideal model delta sigma weight residual 1.528 1.631 -0.102 1.59e-02 3.96e+03 4.15e+01 bond pdb=" CA LEU A 484 " pdb=" C LEU A 484 " ideal model delta sigma weight residual 1.520 1.451 0.070 1.22e-02 6.72e+03 3.26e+01 bond pdb=" C SER A1290 " pdb=" O SER A1290 " ideal model delta sigma weight residual 1.236 1.302 -0.065 1.15e-02 7.56e+03 3.21e+01 bond pdb=" CA THR A 806 " pdb=" CB THR A 806 " ideal model delta sigma weight residual 1.532 1.444 0.087 1.57e-02 4.06e+03 3.11e+01 ... (remaining 47902 not shown) Histogram of bond angle deviations from ideal: 51.61 - 68.73: 2 68.73 - 85.85: 3 85.85 - 102.97: 611 102.97 - 120.09: 44337 120.09 - 137.21: 20452 Bond angle restraints: 65405 Sorted by residual: angle pdb=" C GLN C 6 " pdb=" N PRO C 7 " pdb=" CD PRO C 7 " ideal model delta sigma weight residual 125.00 51.61 73.39 4.10e+00 5.95e-02 3.20e+02 angle pdb=" N ALA I 104 " pdb=" CA ALA I 104 " pdb=" C ALA I 104 " ideal model delta sigma weight residual 112.87 92.38 20.49 1.20e+00 6.94e-01 2.92e+02 angle pdb=" N ASN C 137 " pdb=" CA ASN C 137 " pdb=" C ASN C 137 " ideal model delta sigma weight residual 110.65 89.41 21.24 1.26e+00 6.30e-01 2.84e+02 angle pdb=" N ASP M 94 " pdb=" CA ASP M 94 " pdb=" C ASP M 94 " ideal model delta sigma weight residual 114.09 90.44 23.65 1.55e+00 4.16e-01 2.33e+02 angle pdb=" C HIS I 84 " pdb=" N PRO I 85 " pdb=" CD PRO I 85 " ideal model delta sigma weight residual 125.00 65.08 59.92 4.10e+00 5.95e-02 2.14e+02 ... (remaining 65400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 27590 35.99 - 71.98: 1099 71.98 - 107.96: 80 107.96 - 143.95: 1 143.95 - 179.94: 10 Dihedral angle restraints: 28780 sinusoidal: 13018 harmonic: 15762 Sorted by residual: dihedral pdb=" CA ILE H 99 " pdb=" C ILE H 99 " pdb=" N GLU H 100 " pdb=" CA GLU H 100 " ideal model delta harmonic sigma weight residual 180.00 -85.62 -94.38 0 5.00e+00 4.00e-02 3.56e+02 dihedral pdb=" CA TYR A1308 " pdb=" C TYR A1308 " pdb=" N MET A1309 " pdb=" CA MET A1309 " ideal model delta harmonic sigma weight residual 180.00 137.37 42.63 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA ASN T 123 " pdb=" C ASN T 123 " pdb=" N TYR T 124 " pdb=" CA TYR T 124 " ideal model delta harmonic sigma weight residual 180.00 140.40 39.60 0 5.00e+00 4.00e-02 6.27e+01 ... (remaining 28777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 6998 0.165 - 0.330: 253 0.330 - 0.495: 23 0.495 - 0.660: 8 0.660 - 0.824: 2 Chirality restraints: 7284 Sorted by residual: chirality pdb=" CA THR R 224 " pdb=" N THR R 224 " pdb=" C THR R 224 " pdb=" CB THR R 224 " both_signs ideal model delta sigma weight residual False 2.53 1.70 0.82 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" CA GLU B 77 " pdb=" N GLU B 77 " pdb=" C GLU B 77 " pdb=" CB GLU B 77 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CA SER A 133 " pdb=" N SER A 133 " pdb=" C SER A 133 " pdb=" CB SER A 133 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.04e+01 ... (remaining 7281 not shown) Planarity restraints: 7920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 6 " -0.229 5.00e-02 4.00e+02 2.78e-01 1.23e+02 pdb=" N PRO C 7 " 0.459 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " -0.211 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU P 206 " 0.162 5.00e-02 4.00e+02 2.44e-01 9.51e+01 pdb=" N PRO P 207 " -0.417 5.00e-02 4.00e+02 pdb=" CA PRO P 207 " 0.177 5.00e-02 4.00e+02 pdb=" CD PRO P 207 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 194 " -0.162 5.00e-02 4.00e+02 2.43e-01 9.47e+01 pdb=" N PRO R 195 " 0.416 5.00e-02 4.00e+02 pdb=" CA PRO R 195 " -0.177 5.00e-02 4.00e+02 pdb=" CD PRO R 195 " -0.076 5.00e-02 4.00e+02 ... (remaining 7917 not shown) Histogram of nonbonded interaction distances: 0.53 - 1.40: 13 1.40 - 2.28: 171 2.28 - 3.15: 40121 3.15 - 4.03: 119972 4.03 - 4.90: 215848 Warning: very small nonbonded interaction distances. Nonbonded interactions: 376125 Sorted by model distance: nonbonded pdb=" C VAL Q 131 " pdb="ZN ZN Q 501 " model vdw 0.526 2.460 nonbonded pdb=" OE1 GLN B 90 " pdb=" CG LEU T 141 " model vdw 0.913 3.470 nonbonded pdb=" CA CYS I 17 " pdb="ZN ZN I 201 " model vdw 0.934 2.128 nonbonded pdb=" N ALA M 21 " pdb="ZN ZN M 401 " model vdw 1.025 2.310 nonbonded pdb=" CA VAL J 14 " pdb="ZN ZN J 101 " model vdw 1.051 2.660 ... (remaining 376120 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 11 6.06 5 P 163 5.49 5 Mg 2 5.21 5 S 255 5.16 5 C 28936 2.51 5 N 8194 2.21 5 O 9148 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 15.460 Check model and map are aligned: 0.670 Convert atoms to be neutral: 0.390 Process input model: 143.740 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 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 : 0.011 0.109 47907 Z= 0.700 Angle : 1.732 73.394 65405 Z= 1.086 Chirality : 0.078 0.824 7284 Planarity : 0.013 0.278 7920 Dihedral : 17.237 179.937 18576 Min Nonbonded Distance : 0.526 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 3.77 % Allowed : 8.46 % Favored : 87.77 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.10 (0.10), residues: 5357 helix: -0.59 (0.10), residues: 1877 sheet: -0.46 (0.18), residues: 752 loop : -2.31 (0.11), residues: 2728 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2092 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1935 time to evaluate : 5.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 157 outliers final: 32 residues processed: 2030 average time/residue: 0.6247 time to fit residues: 2006.9466 Evaluate side-chains 1249 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1217 time to evaluate : 5.500 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 32 outliers final: 1 residues processed: 32 average time/residue: 0.5508 time to fit residues: 36.8070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 462 optimal weight: 5.9990 chunk 415 optimal weight: 0.9990 chunk 230 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 280 optimal weight: 0.8980 chunk 221 optimal weight: 0.9980 chunk 429 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 chunk 497 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 188 GLN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN A 735 GLN ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 941 GLN ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS C 140 ASN D 43 HIS D 46 GLN D 66 ASN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 ASN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS I 45 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN K 84 GLN K 89 ASN M 98 ASN ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 ASN O 27 GLN ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 GLN ** S 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 GLN S 145 ASN ** S 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 131 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 47907 Z= 0.320 Angle : 0.924 29.858 65405 Z= 0.480 Chirality : 0.050 0.465 7284 Planarity : 0.008 0.213 7920 Dihedral : 17.983 178.859 7574 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 1.10 % Allowed : 7.43 % Favored : 91.47 % Rotamer Outliers : 4.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.02 % Twisted Proline : 1.23 % 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: -0.93 (0.11), residues: 5357 helix: 0.58 (0.11), residues: 1911 sheet: -0.21 (0.17), residues: 807 loop : -1.69 (0.12), residues: 2639 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1628 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1394 time to evaluate : 5.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 234 outliers final: 130 residues processed: 1524 average time/residue: 0.6128 time to fit residues: 1511.6210 Evaluate side-chains 1278 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1148 time to evaluate : 5.151 Switching outliers to nearest non-outliers outliers start: 130 outliers final: 3 residues processed: 130 average time/residue: 0.4531 time to fit residues: 114.5753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 276 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 414 optimal weight: 0.5980 chunk 338 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 498 optimal weight: 10.0000 chunk 538 optimal weight: 8.9990 chunk 443 optimal weight: 6.9990 chunk 494 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 399 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN B 722 ASN ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS C 140 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN E 132 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN I 46 GLN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 221 ASN M 287 GLN ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 277 HIS ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 145 ASN S 168 ASN ** T 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 47907 Z= 0.299 Angle : 0.853 20.247 65405 Z= 0.439 Chirality : 0.048 0.353 7284 Planarity : 0.007 0.190 7920 Dihedral : 17.776 177.652 7574 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.93 % Favored : 91.15 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.02 % Twisted Proline : 0.82 % 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: -0.78 (0.11), residues: 5357 helix: 0.67 (0.11), residues: 1898 sheet: -0.08 (0.18), residues: 797 loop : -1.58 (0.12), residues: 2662 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1379 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1224 time to evaluate : 5.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 155 outliers final: 80 residues processed: 1315 average time/residue: 0.6298 time to fit residues: 1361.6378 Evaluate side-chains 1162 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1082 time to evaluate : 5.600 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 80 outliers final: 3 residues processed: 80 average time/residue: 0.4621 time to fit residues: 75.3837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 492 optimal weight: 10.0000 chunk 374 optimal weight: 0.7980 chunk 258 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 334 optimal weight: 3.9990 chunk 500 optimal weight: 4.9990 chunk 529 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 474 optimal weight: 20.0000 chunk 142 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN B 312 GLN B 716 HIS B 986 GLN C 66 HIS D 47 GLN E 108 GLN ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN M 156 ASN ** N 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 ASN ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 47907 Z= 0.310 Angle : 0.812 16.628 65405 Z= 0.418 Chirality : 0.047 0.359 7284 Planarity : 0.007 0.178 7920 Dihedral : 17.751 179.139 7574 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.86 % Allowed : 7.58 % Favored : 91.56 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.02 % Twisted Proline : 0.82 % 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: -0.73 (0.11), residues: 5357 helix: 0.65 (0.12), residues: 1903 sheet: -0.00 (0.18), residues: 782 loop : -1.50 (0.12), residues: 2672 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1317 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1173 time to evaluate : 5.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 89 residues processed: 1252 average time/residue: 0.5916 time to fit residues: 1215.1225 Evaluate side-chains 1130 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1041 time to evaluate : 5.157 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 2 residues processed: 89 average time/residue: 0.4174 time to fit residues: 76.5935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 441 optimal weight: 7.9990 chunk 300 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 394 optimal weight: 0.9990 chunk 218 optimal weight: 0.9980 chunk 452 optimal weight: 0.9980 chunk 366 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 475 optimal weight: 9.9990 chunk 133 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN A 735 GLN A 765 ASN ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN M 221 ASN ** N 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 47907 Z= 0.272 Angle : 0.804 14.888 65405 Z= 0.412 Chirality : 0.046 0.331 7284 Planarity : 0.006 0.169 7920 Dihedral : 17.687 178.320 7574 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.93 % Favored : 91.30 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.02 % Twisted Proline : 0.82 % 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: -0.76 (0.11), residues: 5357 helix: 0.66 (0.12), residues: 1896 sheet: -0.09 (0.18), residues: 748 loop : -1.49 (0.12), residues: 2713 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1149 time to evaluate : 5.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 66 residues processed: 1209 average time/residue: 0.6136 time to fit residues: 1216.8725 Evaluate side-chains 1109 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1043 time to evaluate : 5.398 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 2 residues processed: 66 average time/residue: 0.4445 time to fit residues: 62.2064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 178 optimal weight: 0.0020 chunk 477 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 310 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 530 optimal weight: 10.0000 chunk 440 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 175 optimal weight: 0.0980 chunk 278 optimal weight: 1.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN A1190 GLN ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN D 47 GLN ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 221 ASN N 333 ASN ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 GLN S 173 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 47907 Z= 0.252 Angle : 0.797 15.060 65405 Z= 0.409 Chirality : 0.046 0.326 7284 Planarity : 0.006 0.162 7920 Dihedral : 17.615 178.145 7574 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.62 % Favored : 91.66 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.02 % Twisted Proline : 0.82 % 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: -0.68 (0.12), residues: 5357 helix: 0.66 (0.12), residues: 1898 sheet: -0.03 (0.19), residues: 724 loop : -1.39 (0.12), residues: 2735 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1250 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1146 time to evaluate : 5.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 58 residues processed: 1201 average time/residue: 0.6280 time to fit residues: 1243.2163 Evaluate side-chains 1090 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1032 time to evaluate : 5.225 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 2 residues processed: 58 average time/residue: 0.4917 time to fit residues: 59.8059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 511 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 302 optimal weight: 5.9990 chunk 387 optimal weight: 0.9980 chunk 299 optimal weight: 5.9990 chunk 446 optimal weight: 4.9990 chunk 296 optimal weight: 30.0000 chunk 528 optimal weight: 9.9990 chunk 330 optimal weight: 0.1980 chunk 322 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1160 GLN ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 159 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.6307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 47907 Z= 0.332 Angle : 0.825 15.439 65405 Z= 0.423 Chirality : 0.047 0.327 7284 Planarity : 0.006 0.161 7920 Dihedral : 17.638 178.422 7574 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.21 % Favored : 91.10 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.02 % Twisted Proline : 0.82 % 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: -0.77 (0.12), residues: 5357 helix: 0.56 (0.12), residues: 1897 sheet: -0.17 (0.19), residues: 786 loop : -1.42 (0.12), residues: 2674 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1074 time to evaluate : 5.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 53 residues processed: 1111 average time/residue: 0.6068 time to fit residues: 1107.8570 Evaluate side-chains 1065 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1012 time to evaluate : 5.353 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 1 residues processed: 53 average time/residue: 0.4622 time to fit residues: 52.4459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 326 optimal weight: 1.9990 chunk 210 optimal weight: 0.0870 chunk 315 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 335 optimal weight: 0.5980 chunk 359 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 415 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN B 951 GLN B1129 ASN ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 47907 Z= 0.253 Angle : 0.837 25.739 65405 Z= 0.423 Chirality : 0.047 0.364 7284 Planarity : 0.006 0.197 7920 Dihedral : 17.627 178.355 7574 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.71 % Favored : 91.62 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.02 % Twisted Proline : 1.23 % 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: -0.77 (0.12), residues: 5357 helix: 0.55 (0.12), residues: 1907 sheet: -0.18 (0.18), residues: 804 loop : -1.41 (0.12), residues: 2646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1147 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1099 time to evaluate : 5.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 23 residues processed: 1114 average time/residue: 0.6047 time to fit residues: 1104.6036 Evaluate side-chains 1050 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1027 time to evaluate : 5.316 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 1 residues processed: 23 average time/residue: 0.4992 time to fit residues: 27.5028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 480 optimal weight: 5.9990 chunk 506 optimal weight: 6.9990 chunk 461 optimal weight: 6.9990 chunk 492 optimal weight: 6.9990 chunk 505 optimal weight: 0.7980 chunk 296 optimal weight: 30.0000 chunk 214 optimal weight: 0.0770 chunk 386 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 444 optimal weight: 8.9990 chunk 465 optimal weight: 7.9990 overall best weight: 3.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN ** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 145 GLN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN B1049 GLN ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.130 47907 Z= 0.660 Angle : 1.014 18.687 65405 Z= 0.520 Chirality : 0.054 0.347 7284 Planarity : 0.007 0.172 7920 Dihedral : 17.872 179.209 7574 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 30.40 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.71 % Favored : 89.57 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.02 % Twisted Proline : 1.23 % Twisted General : 0.06 % 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: -1.45 (0.11), residues: 5357 helix: -0.02 (0.11), residues: 1901 sheet: -0.62 (0.18), residues: 773 loop : -1.78 (0.12), residues: 2683 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 994 time to evaluate : 5.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 80 residues processed: 1042 average time/residue: 0.6239 time to fit residues: 1063.1010 Evaluate side-chains 1028 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 948 time to evaluate : 5.328 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 1 residues processed: 80 average time/residue: 0.4508 time to fit residues: 76.1966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 490 optimal weight: 6.9990 chunk 323 optimal weight: 0.7980 chunk 520 optimal weight: 20.0000 chunk 317 optimal weight: 0.6980 chunk 246 optimal weight: 0.9990 chunk 361 optimal weight: 4.9990 chunk 545 optimal weight: 5.9990 chunk 502 optimal weight: 8.9990 chunk 434 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 335 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 888 GLN ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN B 951 GLN B1101 GLN ** B1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN C 260 GLN ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 57 ASN ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.6833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 47907 Z= 0.281 Angle : 0.896 16.584 65405 Z= 0.455 Chirality : 0.048 0.378 7284 Planarity : 0.006 0.154 7920 Dihedral : 17.827 179.347 7574 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 23.78 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.10 % Favored : 91.25 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.02 % Twisted Proline : 1.23 % 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: -1.11 (0.11), residues: 5357 helix: 0.28 (0.12), residues: 1893 sheet: -0.54 (0.18), residues: 802 loop : -1.56 (0.12), residues: 2662 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1074 time to evaluate : 5.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 1083 average time/residue: 0.6491 time to fit residues: 1165.0166 Evaluate side-chains 1028 residues out of total 4784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1014 time to evaluate : 5.190 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.5022 time to fit residues: 19.6452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 266 optimal weight: 0.0050 chunk 345 optimal weight: 20.0000 chunk 463 optimal weight: 10.0000 chunk 133 optimal weight: 0.5980 chunk 400 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 435 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 447 optimal weight: 0.1980 chunk 55 optimal weight: 0.9980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 735 GLN ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 GLN B 951 GLN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 352 HIS ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.150145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103167 restraints weight = 102771.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.101498 restraints weight = 66753.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102033 restraints weight = 54882.939| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 47907 Z= 0.245 Angle : 0.881 17.377 65405 Z= 0.446 Chirality : 0.048 0.368 7284 Planarity : 0.006 0.155 7920 Dihedral : 17.725 179.587 7574 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.05 % Favored : 91.32 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.02 % Twisted Proline : 1.23 % Twisted General : 0.06 % 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: -1.04 (0.12), residues: 5357 helix: 0.32 (0.12), residues: 1907 sheet: -0.44 (0.18), residues: 780 loop : -1.53 (0.12), residues: 2670 =============================================================================== Job complete usr+sys time: 17425.30 seconds wall clock time: 308 minutes 44.47 seconds (18524.47 seconds total)