Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 13 09:43:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbq_9792/07_2023/6jbq_9792.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbq_9792/07_2023/6jbq_9792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbq_9792/07_2023/6jbq_9792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbq_9792/07_2023/6jbq_9792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbq_9792/07_2023/6jbq_9792.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbq_9792/07_2023/6jbq_9792.pdb" } resolution = 4.02 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 100 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 17361 2.51 5 N 4982 2.21 5 O 5607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C GLU 413": "OE1" <-> "OE2" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C GLU 477": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 588": "OE1" <-> "OE2" Residue "C GLU 626": "OE1" <-> "OE2" Residue "C ARG 647": "NH1" <-> "NH2" Residue "C GLU 738": "OE1" <-> "OE2" Residue "C GLU 825": "OE1" <-> "OE2" Residue "C GLU 849": "OE1" <-> "OE2" Residue "C GLU 867": "OE1" <-> "OE2" Residue "C GLU 899": "OE1" <-> "OE2" Residue "C ARG 903": "NH1" <-> "NH2" Residue "C GLU 908": "OE1" <-> "OE2" Residue "C ARG 919": "NH1" <-> "NH2" Residue "C GLU 962": "OE1" <-> "OE2" Residue "C GLU 963": "OE1" <-> "OE2" Residue "C GLU 1012": "OE1" <-> "OE2" Residue "C GLU 1020": "OE1" <-> "OE2" Residue "C GLU 1030": "OE1" <-> "OE2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "C ARG 1106": "NH1" <-> "NH2" Residue "C ARG 1171": "NH1" <-> "NH2" Residue "C GLU 1174": "OE1" <-> "OE2" Residue "C GLU 1197": "OE1" <-> "OE2" Residue "C GLU 1274": "OE1" <-> "OE2" Residue "C GLU 1321": "OE1" <-> "OE2" Residue "C GLU 1329": "OE1" <-> "OE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D ARG 314": "NH1" <-> "NH2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "D ARG 425": "NH1" <-> "NH2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "D GLU 532": "OE1" <-> "OE2" Residue "D GLU 556": "OE1" <-> "OE2" Residue "D ARG 634": "NH1" <-> "NH2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D GLU 663": "OE1" <-> "OE2" Residue "D GLU 677": "OE1" <-> "OE2" Residue "D ARG 692": "NH1" <-> "NH2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D GLU 713": "OE1" <-> "OE2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D ARG 836": "NH1" <-> "NH2" Residue "D GLU 866": "OE1" <-> "OE2" Residue "D GLU 874": "OE1" <-> "OE2" Residue "D ARG 933": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D GLU 1052": "OE1" <-> "OE2" Residue "D GLU 1146": "OE1" <-> "OE2" Residue "D ARG 1148": "NH1" <-> "NH2" Residue "D GLU 1187": "OE1" <-> "OE2" Residue "D GLU 1188": "OE1" <-> "OE2" Residue "D GLU 1202": "OE1" <-> "OE2" Residue "D GLU 1205": "OE1" <-> "OE2" Residue "D ARG 1258": "NH1" <-> "NH2" Residue "D GLU 1293": "OE1" <-> "OE2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1317": "OE1" <-> "OE2" Residue "D GLU 1327": "OE1" <-> "OE2" Residue "D ARG 1345": "NH1" <-> "NH2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "F ARG 13": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F GLU 157": "OE1" <-> "OE2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "F ARG 190": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 28163 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1659 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1312, 10320 Classifications: {'peptide': 1312} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1256} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 10331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10331 Classifications: {'peptide': 1335} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1483 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 8, 'TRANS': 177} Chain: "G" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 976 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 975 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Classifications: {'RNA': 5} Modifications used: {'5*END': 1, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14115 SG CYS D 70 108.666 53.521 59.698 1.00 82.04 S ATOM 14129 SG CYS D 72 110.161 52.724 56.967 1.00 89.71 S ATOM 14237 SG CYS D 85 112.115 53.653 60.075 1.00 91.35 S ATOM 14257 SG CYS D 88 111.598 56.634 58.806 1.00 81.03 S ATOM 19909 SG CYS D 814 84.362 73.965 120.932 1.00 62.71 S ATOM 20468 SG CYS D 888 83.493 75.628 116.538 1.00 50.62 S ATOM 20519 SG CYS D 895 84.827 72.639 118.258 1.00 46.75 S ATOM 20540 SG CYS D 898 81.075 75.142 119.104 1.00 44.42 S Time building chain proxies: 13.16, per 1000 atoms: 0.47 Number of scatterers: 28163 At special positions: 0 Unit cell: (133.848, 163.254, 159.198, 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 2 29.99 S 110 16.00 P 100 15.00 Mg 1 11.99 O 5607 8.00 N 4982 7.00 C 17361 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: 11.99 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " Number of angles added : 12 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6192 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 51 sheets defined 36.9% alpha, 14.8% beta 26 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 7.40 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.542A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.707A pdb=" N ALA A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.635A pdb=" N PHE A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.644A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B 41 " --> pdb=" O HIS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.585A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.676A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 removed outlier: 3.668A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 4.158A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE C 57 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.674A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.555A pdb=" N PHE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 291 through 294 removed outlier: 3.523A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 291 through 294' Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.914A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 359 through 371 Processing helix chain 'C' and resid 379 through 389 removed outlier: 4.041A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.640A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.550A pdb=" N ASN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 508 removed outlier: 3.518A pdb=" N ALA C 501 " --> pdb=" O PRO C 497 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 removed outlier: 4.019A pdb=" N LYS C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 4.086A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 684 Processing helix chain 'C' and resid 685 through 689 removed outlier: 3.712A pdb=" N GLN C 688 " --> pdb=" O MET C 685 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA C 689 " --> pdb=" O GLN C 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 685 through 689' Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.825A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 825 removed outlier: 4.248A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 864 removed outlier: 3.633A pdb=" N SER C 863 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 860 through 864' Processing helix chain 'C' and resid 896 through 907 removed outlier: 4.005A pdb=" N LEU C 902 " --> pdb=" O GLU C 898 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 907 " --> pdb=" O ARG C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 979 removed outlier: 3.991A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1038 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.617A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.853A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.661A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1176 removed outlier: 4.224A pdb=" N ARG C1171 " --> pdb=" O GLU C1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.661A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.513A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1300 through 1310 removed outlier: 3.573A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1321 through 1332 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.739A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 94 through 100' Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.609A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.799A pdb=" N ALA D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 264 through 283 removed outlier: 4.248A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.615A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 removed outlier: 3.608A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.590A pdb=" N PHE D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.608A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D 404 " --> pdb=" O MET D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 503 through 515 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.527A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.779A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 592 " --> pdb=" O TYR D 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 588 through 592' Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.826A pdb=" N VAL D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 702 removed outlier: 4.215A pdb=" N ILE D 683 " --> pdb=" O TYR D 679 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.551A pdb=" N SER D 728 " --> pdb=" O MET D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.539A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.782A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR D 786 " --> pdb=" O GLY D 782 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 Processing helix chain 'D' and resid 865 through 876 removed outlier: 3.531A pdb=" N CYS D 869 " --> pdb=" O HIS D 865 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP D 870 " --> pdb=" O GLU D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.082A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 923 " --> pdb=" O ALA D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.577A pdb=" N PHE D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.649A pdb=" N ARG D1222 " --> pdb=" O HIS D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1245 removed outlier: 3.665A pdb=" N THR D1230 " --> pdb=" O VAL D1226 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.347A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1292 removed outlier: 4.200A pdb=" N GLU D1291 " --> pdb=" O ILE D1287 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 removed outlier: 3.926A pdb=" N SER D1313 " --> pdb=" O ILE D1309 " (cutoff:3.500A) Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.675A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY D1339 " --> pdb=" O ALA D1335 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 removed outlier: 3.554A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1371 removed outlier: 3.893A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.846A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 62 through 80 removed outlier: 3.560A pdb=" N VAL E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 17 Processing helix chain 'F' and resid 21 through 38 removed outlier: 3.947A pdb=" N LEU F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG F 28 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS F 31 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS F 32 " --> pdb=" O ARG F 28 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER F 38 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 59 removed outlier: 4.189A pdb=" N VAL F 49 " --> pdb=" O ASP F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.633A pdb=" N SER F 63 " --> pdb=" O ALA F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 3.927A pdb=" N TRP F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 136 Processing helix chain 'F' and resid 139 through 150 Processing helix chain 'F' and resid 155 through 163 removed outlier: 3.629A pdb=" N ILE F 159 " --> pdb=" O SER F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 186 removed outlier: 3.696A pdb=" N VAL F 170 " --> pdb=" O PRO F 166 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS F 184 " --> pdb=" O ALA F 180 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN F 186 " --> pdb=" O ASP F 182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 4.089A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU A 198 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ALA A 189 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 61 removed outlier: 6.403A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 153 removed outlier: 4.291A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 20 removed outlier: 5.460A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 19 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.955A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLY B 151 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.955A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 151 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AB2, first strand: chain 'B' and resid 107 through 111 removed outlier: 3.569A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.657A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 71 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET C 124 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.826A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.861A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.505A pdb=" N ASN C 173 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE C 188 " --> pdb=" O TYR C 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 228 through 230 Processing sheet with id=AB8, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.664A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.818A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.569A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 removed outlier: 7.756A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C 310 " --> pdb=" O TYR C 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.518A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.518A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 623 through 624 removed outlier: 3.676A pdb=" N HIS C 628 " --> pdb=" O ASP C 624 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 634 through 637 Processing sheet with id=AC7, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC8, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.914A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 748 through 752 removed outlier: 7.233A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 817 through 818 removed outlier: 3.662A pdb=" N GLN C 798 " --> pdb=" O MET C1232 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET C1232 " --> pdb=" O GLN C 798 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 830 through 841 removed outlier: 4.022A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.534A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 887 through 888 removed outlier: 3.567A pdb=" N THR C 888 " --> pdb=" O LYS C 914 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD6, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.606A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.606A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1251 through 1252 removed outlier: 3.541A pdb=" N TYR C1251 " --> pdb=" O GLU F 114 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.570A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP D1342 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 34 through 37 removed outlier: 4.820A pdb=" N SER D 34 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N HIS D 104 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY D 36 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLU D 106 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 10.542A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.326A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AE3, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.522A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D 261 " --> pdb=" O VAL D 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 317 through 319 removed outlier: 4.668A pdb=" N SER D 319 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 548 through 557 removed outlier: 3.631A pdb=" N THR D 572 " --> pdb=" O VAL D 548 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.647A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.683A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.931A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AF1, first strand: chain 'D' and resid 1002 through 1003 removed outlier: 3.711A pdb=" N VAL D1002 " --> pdb=" O ASN D1019 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1033 through 1034 removed outlier: 4.123A pdb=" N GLY D1033 " --> pdb=" O ILE D1115 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1059 through 1061 removed outlier: 3.788A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D1123 " --> pdb=" O ILE D1106 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1077 through 1079 Processing sheet with id=AF5, first strand: chain 'D' and resid 1176 through 1178 removed outlier: 3.577A pdb=" N GLY D1161 " --> pdb=" O VAL D1204 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL D1204 " --> pdb=" O GLY D1161 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 1280 through 1281 removed outlier: 6.969A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 967 hydrogen bonds defined for protein. 2790 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 13.08 Time building geometry restraints manager: 12.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8072 1.33 - 1.46: 4868 1.46 - 1.58: 15461 1.58 - 1.70: 198 1.70 - 1.82: 191 Bond restraints: 28790 Sorted by residual: bond pdb=" C3' DA G 29 " pdb=" O3' DA G 29 " ideal model delta sigma weight residual 1.422 1.489 -0.067 3.00e-02 1.11e+03 4.97e+00 bond pdb=" C3' DG G 3 " pdb=" O3' DG G 3 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.12e+00 bond pdb=" C3' DA G 30 " pdb=" O3' DA G 30 " ideal model delta sigma weight residual 1.422 1.482 -0.060 3.00e-02 1.11e+03 4.02e+00 bond pdb=" C3' DA H 43 " pdb=" O3' DA H 43 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.72e+00 bond pdb=" C1' DC H 32 " pdb=" N1 DC H 32 " ideal model delta sigma weight residual 1.490 1.547 -0.057 3.00e-02 1.11e+03 3.61e+00 ... (remaining 28785 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.47: 949 105.47 - 112.64: 15035 112.64 - 119.81: 9894 119.81 - 126.99: 12999 126.99 - 134.16: 451 Bond angle restraints: 39328 Sorted by residual: angle pdb=" C ILE D 856 " pdb=" N LEU D 857 " pdb=" CA LEU D 857 " ideal model delta sigma weight residual 121.54 129.51 -7.97 1.91e+00 2.74e-01 1.74e+01 angle pdb=" CA LEU D1344 " pdb=" CB LEU D1344 " pdb=" CG LEU D1344 " ideal model delta sigma weight residual 116.30 130.52 -14.22 3.50e+00 8.16e-02 1.65e+01 angle pdb=" C LEU D 128 " pdb=" N ASP D 129 " pdb=" CA ASP D 129 " ideal model delta sigma weight residual 122.46 127.97 -5.51 1.41e+00 5.03e-01 1.53e+01 angle pdb=" C LEU D 265 " pdb=" N ASN D 266 " pdb=" CA ASN D 266 " ideal model delta sigma weight residual 120.38 125.61 -5.23 1.37e+00 5.33e-01 1.46e+01 angle pdb=" C ASN C 235 " pdb=" N LYS C 236 " pdb=" CA LYS C 236 " ideal model delta sigma weight residual 121.54 128.82 -7.28 1.91e+00 2.74e-01 1.45e+01 ... (remaining 39323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 16784 35.87 - 71.73: 531 71.73 - 107.60: 25 107.60 - 143.46: 2 143.46 - 179.33: 7 Dihedral angle restraints: 17349 sinusoidal: 7729 harmonic: 9620 Sorted by residual: dihedral pdb=" CA ILE D 856 " pdb=" C ILE D 856 " pdb=" N LEU D 857 " pdb=" CA LEU D 857 " ideal model delta harmonic sigma weight residual -180.00 -157.16 -22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ALA D 426 " pdb=" C ALA D 426 " pdb=" N PRO D 427 " pdb=" CA PRO D 427 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ASP C 189 " pdb=" C ASP C 189 " pdb=" N PRO C 190 " pdb=" CA PRO C 190 " ideal model delta harmonic sigma weight residual 180.00 157.83 22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 17346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3896 0.073 - 0.145: 560 0.145 - 0.218: 46 0.218 - 0.291: 2 0.291 - 0.363: 2 Chirality restraints: 4506 Sorted by residual: chirality pdb=" CB ILE D 500 " pdb=" CA ILE D 500 " pdb=" CG1 ILE D 500 " pdb=" CG2 ILE D 500 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB VAL D1027 " pdb=" CA VAL D1027 " pdb=" CG1 VAL D1027 " pdb=" CG2 VAL D1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB VAL D 407 " pdb=" CA VAL D 407 " pdb=" CG1 VAL D 407 " pdb=" CG2 VAL D 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 4503 not shown) Planarity restraints: 4793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 856 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C ILE D 856 " -0.050 2.00e-02 2.50e+03 pdb=" O ILE D 856 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU D 857 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 850 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO D 851 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 851 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 851 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 501 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO D 502 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " -0.034 5.00e-02 4.00e+02 ... (remaining 4790 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1733 2.74 - 3.28: 24517 3.28 - 3.82: 44541 3.82 - 4.36: 50421 4.36 - 4.90: 86384 Nonbonded interactions: 207596 Sorted by model distance: nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1501 " model vdw 2.197 2.170 nonbonded pdb=" OG SER C 576 " pdb=" O GLN C 659 " model vdw 2.303 2.440 nonbonded pdb=" OG SER C 646 " pdb=" OD1 ASP C 648 " model vdw 2.307 2.440 nonbonded pdb=" O SER D 191 " pdb=" OG SER D 191 " model vdw 2.322 2.440 nonbonded pdb=" O LYS C 476 " pdb=" OG SER C 480 " model vdw 2.331 2.440 ... (remaining 207591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 138 or (resid 139 and (name N or name CA or name \ C or name O or name CB )) or resid 140 through 232)) selection = (chain 'B' and (resid 8 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 135 or (resid 136 and (name N or \ name CA or name C or name O or name CB )) or resid 137 through 158 or resid 170 \ through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.750 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 80.800 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 28790 Z= 0.207 Angle : 0.701 14.221 39328 Z= 0.391 Chirality : 0.049 0.363 4506 Planarity : 0.006 0.064 4793 Dihedral : 16.327 179.326 11157 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.11), residues: 3325 helix: -3.01 (0.09), residues: 1135 sheet: -1.43 (0.23), residues: 396 loop : -2.92 (0.11), residues: 1794 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 721 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 730 average time/residue: 0.4605 time to fit residues: 507.1555 Evaluate side-chains 395 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 391 time to evaluate : 3.018 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2485 time to fit residues: 6.1378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 20.0000 chunk 256 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 173 optimal weight: 0.0470 chunk 137 optimal weight: 4.9990 chunk 265 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 227 GLN B 132 HIS C 150 HIS C 462 ASN C 832 HIS C1009 ASN C1157 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 HIS D 477 GLN D 702 GLN D 739 GLN D 817 HIS D 954 ASN D 979 ASN D1044 GLN D1114 GLN ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN E 43 ASN ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 28790 Z= 0.320 Angle : 0.627 7.920 39328 Z= 0.334 Chirality : 0.044 0.173 4506 Planarity : 0.005 0.073 4793 Dihedral : 16.136 179.505 4674 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.13), residues: 3325 helix: -0.59 (0.14), residues: 1150 sheet: -1.12 (0.24), residues: 399 loop : -2.42 (0.12), residues: 1776 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 442 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 444 average time/residue: 0.4063 time to fit residues: 284.6211 Evaluate side-chains 311 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 2.998 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 256 optimal weight: 30.0000 chunk 209 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 308 optimal weight: 6.9990 chunk 333 optimal weight: 10.0000 chunk 274 optimal weight: 0.0570 chunk 305 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 overall best weight: 3.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS B 147 GLN B 227 GLN C 462 ASN C 513 GLN C 824 GLN C1090 ASN C1157 GLN C1220 GLN C1268 GLN C1299 ASN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN D 777 HIS ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1289 ASN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 28790 Z= 0.285 Angle : 0.581 8.627 39328 Z= 0.306 Chirality : 0.043 0.278 4506 Planarity : 0.004 0.078 4793 Dihedral : 16.115 178.551 4674 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3325 helix: 0.25 (0.15), residues: 1162 sheet: -1.08 (0.25), residues: 404 loop : -2.27 (0.13), residues: 1759 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 411 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 412 average time/residue: 0.4223 time to fit residues: 277.3487 Evaluate side-chains 297 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 296 time to evaluate : 3.292 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2544 time to fit residues: 4.8465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 304 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 160 optimal weight: 0.3980 chunk 34 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 309 optimal weight: 9.9990 chunk 327 optimal weight: 7.9990 chunk 161 optimal weight: 0.9980 chunk 293 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 GLN B 227 GLN C 513 GLN C 604 HIS C 686 GLN C1090 ASN C1136 GLN C1157 GLN C1220 GLN C1299 ASN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 28790 Z= 0.157 Angle : 0.511 7.453 39328 Z= 0.270 Chirality : 0.041 0.190 4506 Planarity : 0.004 0.074 4793 Dihedral : 16.005 176.997 4674 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3325 helix: 0.83 (0.16), residues: 1154 sheet: -0.85 (0.25), residues: 400 loop : -2.02 (0.13), residues: 1771 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 427 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 428 average time/residue: 0.4092 time to fit residues: 282.0193 Evaluate side-chains 309 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 3.133 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 243 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 279 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 294 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 GLN C 343 HIS C 462 ASN C 513 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C1157 GLN C1209 GLN C1299 ASN D 739 GLN D 777 HIS D 897 HIS ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 28790 Z= 0.420 Angle : 0.685 12.173 39328 Z= 0.357 Chirality : 0.045 0.241 4506 Planarity : 0.005 0.080 4793 Dihedral : 16.214 178.637 4674 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3325 helix: 0.76 (0.15), residues: 1151 sheet: -0.90 (0.25), residues: 418 loop : -2.08 (0.13), residues: 1756 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 379 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 379 average time/residue: 0.4098 time to fit residues: 250.3502 Evaluate side-chains 277 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 3.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 0.6980 chunk 295 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 327 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 147 GLN C 462 ASN C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C1157 GLN C1299 ASN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 28790 Z= 0.164 Angle : 0.535 7.280 39328 Z= 0.281 Chirality : 0.041 0.199 4506 Planarity : 0.004 0.083 4793 Dihedral : 16.082 176.826 4674 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3325 helix: 1.12 (0.16), residues: 1156 sheet: -0.67 (0.25), residues: 427 loop : -1.87 (0.13), residues: 1742 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 397 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 398 average time/residue: 0.4014 time to fit residues: 258.1841 Evaluate side-chains 307 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 3.188 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 316 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 239 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 chunk 276 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 326 optimal weight: 0.4980 chunk 204 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 147 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C1288 GLN C1299 ASN D 340 GLN D 777 HIS ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 28790 Z= 0.202 Angle : 0.548 7.282 39328 Z= 0.287 Chirality : 0.041 0.184 4506 Planarity : 0.004 0.083 4793 Dihedral : 16.056 176.499 4674 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3325 helix: 1.24 (0.16), residues: 1156 sheet: -0.60 (0.25), residues: 422 loop : -1.80 (0.14), residues: 1747 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 382 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 383 average time/residue: 0.4096 time to fit residues: 255.8044 Evaluate side-chains 301 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 3.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 195 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 chunk 161 optimal weight: 0.0670 chunk 30 optimal weight: 8.9990 chunk 256 optimal weight: 0.0040 overall best weight: 1.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 147 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN C1288 GLN C1299 ASN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN F 183 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 28790 Z= 0.165 Angle : 0.525 7.527 39328 Z= 0.274 Chirality : 0.041 0.165 4506 Planarity : 0.004 0.083 4793 Dihedral : 16.014 176.134 4674 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3325 helix: 1.38 (0.16), residues: 1150 sheet: -0.49 (0.26), residues: 420 loop : -1.71 (0.14), residues: 1755 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 385 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 386 average time/residue: 0.3975 time to fit residues: 253.5689 Evaluate side-chains 311 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 2.930 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 0.6980 chunk 313 optimal weight: 20.0000 chunk 285 optimal weight: 20.0000 chunk 304 optimal weight: 4.9990 chunk 312 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 132 optimal weight: 0.0870 chunk 239 optimal weight: 20.0000 chunk 93 optimal weight: 0.4980 chunk 275 optimal weight: 40.0000 chunk 287 optimal weight: 9.9990 overall best weight: 2.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 147 GLN C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN C1209 GLN C1288 GLN C1299 ASN D 777 HIS ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 28790 Z= 0.196 Angle : 0.542 7.951 39328 Z= 0.283 Chirality : 0.042 0.210 4506 Planarity : 0.004 0.084 4793 Dihedral : 16.017 177.375 4674 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3325 helix: 1.40 (0.16), residues: 1150 sheet: -0.49 (0.26), residues: 420 loop : -1.67 (0.14), residues: 1755 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 384 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 387 average time/residue: 0.4049 time to fit residues: 255.6448 Evaluate side-chains 299 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 3.340 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 0.4980 chunk 199 optimal weight: 4.9990 chunk 321 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 223 optimal weight: 0.0980 chunk 337 optimal weight: 10.0000 chunk 310 optimal weight: 8.9990 chunk 268 optimal weight: 40.0000 chunk 27 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 GLN C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 GLN C1299 ASN D 777 HIS ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 28790 Z= 0.197 Angle : 0.542 9.529 39328 Z= 0.283 Chirality : 0.042 0.161 4506 Planarity : 0.004 0.084 4793 Dihedral : 16.017 178.237 4674 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3325 helix: 1.44 (0.16), residues: 1149 sheet: -0.50 (0.26), residues: 415 loop : -1.65 (0.14), residues: 1761 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 381 time to evaluate : 3.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.4020 time to fit residues: 252.1154 Evaluate side-chains 301 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.982 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 164 optimal weight: 0.0010 chunk 213 optimal weight: 0.9980 chunk 286 optimal weight: 30.0000 chunk 82 optimal weight: 0.8980 chunk 247 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 74 optimal weight: 0.0070 chunk 269 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 276 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 GLN C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN C1209 GLN C1288 GLN C1299 ASN D 777 HIS ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1366 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN F 183 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.148778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.122078 restraints weight = 47587.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121064 restraints weight = 59825.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121869 restraints weight = 66924.922| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 28790 Z= 0.141 Angle : 0.533 10.000 39328 Z= 0.275 Chirality : 0.041 0.239 4506 Planarity : 0.003 0.082 4793 Dihedral : 15.933 177.858 4674 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3325 helix: 1.53 (0.16), residues: 1154 sheet: -0.39 (0.26), residues: 411 loop : -1.55 (0.14), residues: 1760 =============================================================================== Job complete usr+sys time: 5616.30 seconds wall clock time: 102 minutes 51.56 seconds (6171.56 seconds total)