Starting phenix.real_space_refine on Wed Mar 20 18:03:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbq_9792/03_2024/6jbq_9792.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbq_9792/03_2024/6jbq_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_9792/03_2024/6jbq_9792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbq_9792/03_2024/6jbq_9792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbq_9792/03_2024/6jbq_9792.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbq_9792/03_2024/6jbq_9792.pdb" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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-dev-5265/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: 17 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: 15.10, per 1000 atoms: 0.54 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: 13.19 Conformation dependent library (CDL) restraints added in 5.8 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: 9.96 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: 13.22 Time building geometry restraints manager: 13.31 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: 16885 35.87 - 71.73: 552 71.73 - 107.60: 27 107.60 - 143.46: 2 143.46 - 179.33: 7 Dihedral angle restraints: 17473 sinusoidal: 7853 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 17470 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: 0.570 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: 4.020 Check model and map are aligned: 0.410 Set scattering table: 0.220 Process input model: 87.560 Find NCS groups from input model: 1.050 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.850 ------------------------------------------------------------------------------- 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 : 16.540 179.326 11281 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 % Allowed : 5.91 % Favored : 93.71 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1193 HIS 0.007 0.001 HIS C 150 PHE 0.016 0.001 PHE D1325 TYR 0.011 0.001 TYR D 631 ARG 0.006 0.000 ARG D 259 *********************** 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 : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 VAL cc_start: 0.8384 (t) cc_final: 0.8139 (p) REVERT: A 177 TYR cc_start: 0.7413 (m-80) cc_final: 0.6846 (m-10) REVERT: B 16 ILE cc_start: 0.8782 (mt) cc_final: 0.8476 (pt) REVERT: B 147 GLN cc_start: 0.8540 (pt0) cc_final: 0.7401 (pt0) REVERT: C 85 CYS cc_start: 0.8263 (m) cc_final: 0.8042 (t) REVERT: C 156 PHE cc_start: 0.8281 (m-80) cc_final: 0.8078 (m-10) REVERT: C 439 LYS cc_start: 0.7702 (ptpt) cc_final: 0.7303 (pptt) REVERT: C 488 MET cc_start: 0.7716 (tpp) cc_final: 0.7234 (tpt) REVERT: C 654 ASP cc_start: 0.6790 (t0) cc_final: 0.6542 (t0) REVERT: C 768 MET cc_start: 0.8364 (mtp) cc_final: 0.8029 (mtm) REVERT: C 785 ASP cc_start: 0.7867 (m-30) cc_final: 0.7125 (p0) REVERT: C 808 ASN cc_start: 0.8949 (m110) cc_final: 0.8712 (m-40) REVERT: C 949 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6733 (mm-30) REVERT: C 1080 ASN cc_start: 0.8411 (m-40) cc_final: 0.7878 (m-40) REVERT: C 1088 ASP cc_start: 0.8138 (p0) cc_final: 0.7832 (p0) REVERT: C 1230 MET cc_start: 0.8713 (ttm) cc_final: 0.8489 (ttt) REVERT: C 1273 MET cc_start: 0.7850 (mtp) cc_final: 0.7643 (mtm) REVERT: C 1274 GLU cc_start: 0.7859 (mp0) cc_final: 0.7554 (mp0) REVERT: D 527 LEU cc_start: 0.8324 (mm) cc_final: 0.8026 (mm) REVERT: D 872 LEU cc_start: 0.8077 (tt) cc_final: 0.7832 (tt) REVERT: D 1196 LEU cc_start: 0.7688 (mm) cc_final: 0.7437 (mm) REVERT: D 1302 TYR cc_start: 0.8048 (p90) cc_final: 0.7819 (p90) REVERT: D 1327 GLU cc_start: 0.8005 (tt0) cc_final: 0.7763 (tt0) REVERT: F 20 LYS cc_start: 0.8369 (mttp) cc_final: 0.7927 (tptt) REVERT: F 77 ILE cc_start: 0.8905 (mt) cc_final: 0.8636 (tp) REVERT: F 99 ASP cc_start: 0.8556 (t0) cc_final: 0.8019 (t70) REVERT: F 101 ILE cc_start: 0.8656 (mt) cc_final: 0.8251 (mp) outliers start: 11 outliers final: 4 residues processed: 730 average time/residue: 0.4478 time to fit residues: 489.1600 Evaluate side-chains 402 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 398 time to evaluate : 3.321 ------------------------------------------------------------------------------- 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: 30.0000 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: 9.9990 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: 4.0086 ------------------------------------------------------------------------------- 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 ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS C 462 ASN C 832 HIS C1009 ASN C1157 GLN C1268 GLN ** 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 D1044 GLN D1114 GLN ** D1126 GLN ** 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: 0.8028 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 28790 Z= 0.326 Angle : 0.634 8.211 39328 Z= 0.336 Chirality : 0.044 0.170 4506 Planarity : 0.005 0.073 4793 Dihedral : 16.551 179.534 4798 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.07 % Allowed : 6.22 % Favored : 93.71 % 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: -2.34 (0.13), residues: 3325 helix: -0.54 (0.14), residues: 1147 sheet: -1.13 (0.24), residues: 399 loop : -2.42 (0.12), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1193 HIS 0.018 0.002 HIS D 545 PHE 0.020 0.002 PHE D 437 TYR 0.017 0.002 TYR F 71 ARG 0.007 0.001 ARG C1246 *********************** 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 451 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 449 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASN cc_start: 0.8677 (t0) cc_final: 0.8465 (t0) REVERT: A 177 TYR cc_start: 0.7696 (m-80) cc_final: 0.7176 (m-10) REVERT: B 10 LYS cc_start: 0.8164 (mppt) cc_final: 0.7561 (mppt) REVERT: B 16 ILE cc_start: 0.8945 (mt) cc_final: 0.8728 (pt) REVERT: B 68 TYR cc_start: 0.9069 (m-80) cc_final: 0.8835 (m-80) REVERT: C 195 PHE cc_start: 0.7364 (m-80) cc_final: 0.6914 (m-80) REVERT: C 347 ILE cc_start: 0.8351 (mm) cc_final: 0.8099 (mm) REVERT: C 739 ASP cc_start: 0.8505 (p0) cc_final: 0.8262 (p0) REVERT: C 768 MET cc_start: 0.8328 (mtp) cc_final: 0.8097 (mtm) REVERT: C 785 ASP cc_start: 0.7891 (m-30) cc_final: 0.7158 (p0) REVERT: C 1180 MET cc_start: 0.9126 (tpp) cc_final: 0.8786 (ttm) REVERT: C 1230 MET cc_start: 0.8652 (ttm) cc_final: 0.8318 (ttt) REVERT: C 1273 MET cc_start: 0.8064 (mtp) cc_final: 0.7801 (mtm) REVERT: C 1274 GLU cc_start: 0.7904 (mp0) cc_final: 0.7556 (mp0) REVERT: D 263 SER cc_start: 0.9571 (m) cc_final: 0.9359 (t) REVERT: D 457 TYR cc_start: 0.8747 (m-80) cc_final: 0.8301 (m-80) REVERT: D 527 LEU cc_start: 0.8353 (mm) cc_final: 0.8108 (mm) REVERT: D 532 GLU cc_start: 0.8338 (tp30) cc_final: 0.7917 (tp30) REVERT: D 1199 PHE cc_start: 0.7053 (m-10) cc_final: 0.6723 (m-10) REVERT: D 1349 GLU cc_start: 0.7825 (pt0) cc_final: 0.7484 (mt-10) REVERT: E 18 ASP cc_start: 0.7297 (p0) cc_final: 0.6985 (p0) REVERT: F 20 LYS cc_start: 0.8486 (mttp) cc_final: 0.7972 (tptt) REVERT: F 99 ASP cc_start: 0.8602 (t0) cc_final: 0.8265 (t70) REVERT: F 101 ILE cc_start: 0.8738 (mt) cc_final: 0.8482 (mp) outliers start: 2 outliers final: 0 residues processed: 451 average time/residue: 0.4046 time to fit residues: 287.0443 Evaluate side-chains 318 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 3.454 ------------------------------------------------------------------------------- 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: 3.9990 chunk 95 optimal weight: 7.9990 chunk 256 optimal weight: 30.0000 chunk 209 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 333 optimal weight: 10.0000 chunk 274 optimal weight: 0.0970 chunk 305 optimal weight: 0.5980 chunk 105 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 649 GLN C 824 GLN C1090 ASN C1157 GLN C1220 GLN C1299 ASN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN D 777 HIS D 979 ASN ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1289 ASN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28790 Z= 0.187 Angle : 0.529 7.747 39328 Z= 0.279 Chirality : 0.042 0.223 4506 Planarity : 0.004 0.076 4793 Dihedral : 16.447 178.041 4798 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.11 % Allowed : 3.57 % Favored : 96.32 % 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: -1.57 (0.14), residues: 3325 helix: 0.42 (0.15), residues: 1157 sheet: -0.92 (0.25), residues: 404 loop : -2.15 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1193 HIS 0.007 0.001 HIS B 23 PHE 0.016 0.001 PHE B 35 TYR 0.011 0.001 TYR D 631 ARG 0.004 0.000 ARG D1174 *********************** 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 432 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 429 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.7885 (t0) cc_final: 0.7678 (t0) REVERT: C 8 LYS cc_start: 0.8735 (mttt) cc_final: 0.8307 (ttmm) REVERT: C 295 LYS cc_start: 0.7085 (mmtt) cc_final: 0.6857 (mmtp) REVERT: C 347 ILE cc_start: 0.8245 (mm) cc_final: 0.7792 (mm) REVERT: C 559 CYS cc_start: 0.9500 (t) cc_final: 0.9239 (t) REVERT: C 768 MET cc_start: 0.8239 (mtp) cc_final: 0.7974 (mtm) REVERT: C 785 ASP cc_start: 0.7893 (m-30) cc_final: 0.7104 (p0) REVERT: C 1230 MET cc_start: 0.8727 (ttm) cc_final: 0.8439 (ttt) REVERT: C 1273 MET cc_start: 0.7980 (mtp) cc_final: 0.7729 (mtm) REVERT: C 1274 GLU cc_start: 0.7880 (mp0) cc_final: 0.7584 (mp0) REVERT: D 263 SER cc_start: 0.9608 (m) cc_final: 0.9386 (t) REVERT: D 457 TYR cc_start: 0.8680 (m-80) cc_final: 0.8286 (m-80) REVERT: D 527 LEU cc_start: 0.8516 (mm) cc_final: 0.8303 (mm) REVERT: D 532 GLU cc_start: 0.8298 (tp30) cc_final: 0.7850 (tp30) REVERT: D 1199 PHE cc_start: 0.6923 (m-10) cc_final: 0.6589 (m-10) REVERT: D 1363 TYR cc_start: 0.7885 (t80) cc_final: 0.7643 (t80) REVERT: E 18 ASP cc_start: 0.7238 (p0) cc_final: 0.6891 (p0) REVERT: F 20 LYS cc_start: 0.8458 (mttp) cc_final: 0.7932 (tptt) REVERT: F 163 MET cc_start: 0.6804 (mmt) cc_final: 0.6586 (ttt) outliers start: 3 outliers final: 0 residues processed: 429 average time/residue: 0.3940 time to fit residues: 268.2409 Evaluate side-chains 309 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 3.067 ------------------------------------------------------------------------------- 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: 1.9990 chunk 160 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 147 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 309 optimal weight: 10.0000 chunk 327 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 293 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 649 GLN C1090 ASN C1136 GLN C1157 GLN C1299 ASN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8023 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28790 Z= 0.178 Angle : 0.515 7.563 39328 Z= 0.271 Chirality : 0.041 0.183 4506 Planarity : 0.004 0.074 4793 Dihedral : 16.363 177.281 4798 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.07 % Allowed : 2.72 % Favored : 97.21 % 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: -1.13 (0.14), residues: 3325 helix: 0.95 (0.16), residues: 1149 sheet: -0.79 (0.26), residues: 393 loop : -1.97 (0.13), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1193 HIS 0.003 0.001 HIS D 777 PHE 0.015 0.001 PHE C 514 TYR 0.017 0.001 TYR C1018 ARG 0.006 0.000 ARG D 838 *********************** 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 413 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 411 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.7920 (t0) cc_final: 0.7679 (t0) REVERT: C 8 LYS cc_start: 0.8802 (mttt) cc_final: 0.8405 (ttmm) REVERT: C 347 ILE cc_start: 0.8472 (mm) cc_final: 0.7918 (mm) REVERT: C 524 ILE cc_start: 0.9038 (tt) cc_final: 0.8807 (tt) REVERT: C 559 CYS cc_start: 0.9516 (t) cc_final: 0.9269 (t) REVERT: C 737 ASN cc_start: 0.8281 (t0) cc_final: 0.7901 (t0) REVERT: C 768 MET cc_start: 0.8275 (mtp) cc_final: 0.7983 (mtm) REVERT: C 785 ASP cc_start: 0.7897 (m-30) cc_final: 0.7106 (p0) REVERT: C 1180 MET cc_start: 0.8822 (ttm) cc_final: 0.8610 (ttm) REVERT: C 1273 MET cc_start: 0.7940 (mtp) cc_final: 0.7701 (mtm) REVERT: C 1274 GLU cc_start: 0.7860 (mp0) cc_final: 0.7446 (mp0) REVERT: D 263 SER cc_start: 0.9638 (m) cc_final: 0.9394 (t) REVERT: D 457 TYR cc_start: 0.8683 (m-80) cc_final: 0.8315 (m-80) REVERT: D 527 LEU cc_start: 0.8643 (mm) cc_final: 0.8404 (mm) REVERT: D 532 GLU cc_start: 0.8322 (tp30) cc_final: 0.7872 (tp30) REVERT: D 1199 PHE cc_start: 0.6929 (m-10) cc_final: 0.6575 (m-10) REVERT: D 1363 TYR cc_start: 0.7969 (t80) cc_final: 0.7636 (t80) REVERT: E 18 ASP cc_start: 0.7272 (p0) cc_final: 0.6884 (p0) REVERT: F 20 LYS cc_start: 0.8498 (mttp) cc_final: 0.7936 (tptt) REVERT: F 163 MET cc_start: 0.6868 (mmt) cc_final: 0.6632 (ttt) REVERT: F 175 PHE cc_start: 0.8860 (t80) cc_final: 0.8510 (t80) outliers start: 2 outliers final: 0 residues processed: 411 average time/residue: 0.3619 time to fit residues: 242.3654 Evaluate side-chains 315 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 3.030 ------------------------------------------------------------------------------- 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: 1.9990 chunk 186 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 226 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 294 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 343 HIS C 513 GLN C 649 GLN C 824 GLN C1090 ASN C1157 GLN C1209 GLN C1299 ASN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28790 Z= 0.336 Angle : 0.634 10.080 39328 Z= 0.331 Chirality : 0.044 0.213 4506 Planarity : 0.004 0.080 4793 Dihedral : 16.520 178.447 4798 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.07 % Allowed : 3.89 % Favored : 96.04 % 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: -1.19 (0.14), residues: 3325 helix: 0.88 (0.16), residues: 1158 sheet: -0.81 (0.25), residues: 418 loop : -2.03 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 409 HIS 0.007 0.001 HIS D 777 PHE 0.029 0.002 PHE C1265 TYR 0.015 0.002 TYR D 349 ARG 0.013 0.001 ARG D 838 *********************** 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 402 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 400 time to evaluate : 3.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.7994 (t0) cc_final: 0.7734 (t0) REVERT: C 8 LYS cc_start: 0.8880 (mttt) cc_final: 0.8329 (ttmm) REVERT: C 132 ASP cc_start: 0.7862 (t0) cc_final: 0.7562 (t0) REVERT: C 347 ILE cc_start: 0.8596 (mm) cc_final: 0.7987 (mm) REVERT: C 559 CYS cc_start: 0.9526 (t) cc_final: 0.9243 (t) REVERT: C 685 MET cc_start: 0.8742 (mtm) cc_final: 0.8457 (mtm) REVERT: C 739 ASP cc_start: 0.8401 (p0) cc_final: 0.8183 (p0) REVERT: C 768 MET cc_start: 0.8254 (mtp) cc_final: 0.8017 (mtm) REVERT: C 785 ASP cc_start: 0.7914 (m-30) cc_final: 0.7081 (p0) REVERT: C 1273 MET cc_start: 0.8064 (mtp) cc_final: 0.7845 (mtm) REVERT: C 1274 GLU cc_start: 0.7883 (mp0) cc_final: 0.7539 (mp0) REVERT: C 1319 MET cc_start: 0.8791 (tpp) cc_final: 0.8144 (ttp) REVERT: D 457 TYR cc_start: 0.8771 (m-80) cc_final: 0.8363 (m-80) REVERT: D 527 LEU cc_start: 0.8760 (mm) cc_final: 0.8542 (mm) REVERT: D 532 GLU cc_start: 0.8302 (tp30) cc_final: 0.7924 (tp30) REVERT: D 738 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7169 (ptm-80) REVERT: D 805 GLN cc_start: 0.8691 (pp30) cc_final: 0.8333 (pp30) REVERT: D 1196 LEU cc_start: 0.8243 (mm) cc_final: 0.7524 (tp) REVERT: D 1199 PHE cc_start: 0.7182 (m-10) cc_final: 0.6853 (m-10) REVERT: D 1334 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7505 (tm-30) REVERT: E 15 ASN cc_start: 0.8101 (t0) cc_final: 0.7894 (t0) REVERT: E 18 ASP cc_start: 0.7301 (p0) cc_final: 0.6941 (p0) REVERT: F 20 LYS cc_start: 0.8655 (mttp) cc_final: 0.7998 (tptt) REVERT: F 23 ASN cc_start: 0.8636 (p0) cc_final: 0.8202 (m-40) REVERT: F 67 ASP cc_start: 0.7309 (m-30) cc_final: 0.7045 (t0) REVERT: F 101 ILE cc_start: 0.8773 (mp) cc_final: 0.8543 (mp) REVERT: F 163 MET cc_start: 0.6977 (mmt) cc_final: 0.6718 (ttt) outliers start: 2 outliers final: 0 residues processed: 400 average time/residue: 0.4342 time to fit residues: 277.0022 Evaluate side-chains 294 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 3.114 ------------------------------------------------------------------------------- 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: 3.9990 chunk 295 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 192 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 327 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 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 41 ASN A 227 GLN B 147 GLN C 513 GLN C 649 GLN ** 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** ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8091 moved from start: 0.4093 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= 0.198 Angle : 0.546 10.776 39328 Z= 0.286 Chirality : 0.042 0.202 4506 Planarity : 0.004 0.082 4793 Dihedral : 16.422 177.118 4798 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.04 % Allowed : 2.16 % Favored : 97.81 % 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: -0.90 (0.14), residues: 3325 helix: 1.13 (0.16), residues: 1153 sheet: -0.63 (0.25), residues: 416 loop : -1.86 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1193 HIS 0.003 0.001 HIS D 430 PHE 0.029 0.001 PHE C 186 TYR 0.017 0.001 TYR C 73 ARG 0.007 0.000 ARG C 180 *********************** 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 396 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 395 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.7947 (t0) cc_final: 0.7662 (t0) REVERT: C 8 LYS cc_start: 0.8871 (mttt) cc_final: 0.8305 (ttmm) REVERT: C 132 ASP cc_start: 0.7746 (t0) cc_final: 0.7483 (t0) REVERT: C 195 PHE cc_start: 0.7337 (m-80) cc_final: 0.6909 (m-80) REVERT: C 347 ILE cc_start: 0.8529 (mm) cc_final: 0.7967 (mm) REVERT: C 370 MET cc_start: 0.8189 (mmp) cc_final: 0.7868 (mmm) REVERT: C 559 CYS cc_start: 0.9568 (t) cc_final: 0.9207 (t) REVERT: C 768 MET cc_start: 0.8201 (mtp) cc_final: 0.7954 (mtm) REVERT: C 785 ASP cc_start: 0.7946 (m-30) cc_final: 0.6985 (p0) REVERT: C 796 LEU cc_start: 0.9371 (mp) cc_final: 0.9153 (mt) REVERT: C 1274 GLU cc_start: 0.7803 (mp0) cc_final: 0.7472 (mp0) REVERT: C 1319 MET cc_start: 0.8837 (tpp) cc_final: 0.8176 (ttp) REVERT: D 457 TYR cc_start: 0.8727 (m-80) cc_final: 0.8420 (m-80) REVERT: D 527 LEU cc_start: 0.8853 (mm) cc_final: 0.8586 (mm) REVERT: D 532 GLU cc_start: 0.8370 (tp30) cc_final: 0.7894 (tp30) REVERT: D 1196 LEU cc_start: 0.8291 (mm) cc_final: 0.7601 (tp) REVERT: D 1199 PHE cc_start: 0.7114 (m-10) cc_final: 0.6825 (m-10) REVERT: E 18 ASP cc_start: 0.7255 (p0) cc_final: 0.6892 (p0) REVERT: E 44 ASP cc_start: 0.8169 (m-30) cc_final: 0.7906 (m-30) REVERT: F 20 LYS cc_start: 0.8563 (mttp) cc_final: 0.7998 (tptt) REVERT: F 77 ILE cc_start: 0.9008 (mt) cc_final: 0.8597 (tp) REVERT: F 175 PHE cc_start: 0.8783 (t80) cc_final: 0.8455 (t80) outliers start: 1 outliers final: 0 residues processed: 395 average time/residue: 0.3812 time to fit residues: 242.1275 Evaluate side-chains 310 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 3.542 ------------------------------------------------------------------------------- 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: 1.9990 chunk 36 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 276 optimal weight: 20.0000 chunk 183 optimal weight: 0.9980 chunk 326 optimal weight: 20.0000 chunk 204 optimal weight: 0.7980 chunk 199 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 GLN B 227 GLN C 604 HIS C 649 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C1288 GLN C1299 ASN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN D 777 HIS ** D1126 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28790 Z= 0.174 Angle : 0.540 12.008 39328 Z= 0.281 Chirality : 0.041 0.171 4506 Planarity : 0.004 0.084 4793 Dihedral : 16.362 176.415 4798 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.04 % Allowed : 1.41 % Favored : 98.55 % 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: -0.71 (0.14), residues: 3325 helix: 1.31 (0.16), residues: 1143 sheet: -0.53 (0.26), residues: 415 loop : -1.75 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D1193 HIS 0.009 0.001 HIS D 777 PHE 0.027 0.001 PHE C 186 TYR 0.017 0.001 TYR C 73 ARG 0.009 0.000 ARG D 101 *********************** 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 403 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 402 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.7918 (t0) cc_final: 0.7669 (t0) REVERT: B 51 MET cc_start: 0.8161 (mmm) cc_final: 0.7951 (tpt) REVERT: C 8 LYS cc_start: 0.8863 (mttt) cc_final: 0.8155 (ttpp) REVERT: C 132 ASP cc_start: 0.7868 (t0) cc_final: 0.7524 (t0) REVERT: C 347 ILE cc_start: 0.8505 (mm) cc_final: 0.7957 (mm) REVERT: C 370 MET cc_start: 0.8217 (mmp) cc_final: 0.7908 (mmm) REVERT: C 685 MET cc_start: 0.8636 (mtm) cc_final: 0.8351 (mtm) REVERT: C 704 MET cc_start: 0.8092 (mmm) cc_final: 0.7813 (mmp) REVERT: C 739 ASP cc_start: 0.8335 (p0) cc_final: 0.8090 (p0) REVERT: C 785 ASP cc_start: 0.7942 (m-30) cc_final: 0.7194 (p0) REVERT: C 1274 GLU cc_start: 0.7834 (mp0) cc_final: 0.7420 (mp0) REVERT: C 1319 MET cc_start: 0.8802 (tpp) cc_final: 0.8169 (ttp) REVERT: D 330 MET cc_start: 0.7900 (ttm) cc_final: 0.7636 (ttm) REVERT: D 457 TYR cc_start: 0.8691 (m-80) cc_final: 0.8451 (m-80) REVERT: D 527 LEU cc_start: 0.8834 (mm) cc_final: 0.8541 (mt) REVERT: D 532 GLU cc_start: 0.8307 (tp30) cc_final: 0.8046 (mm-30) REVERT: D 890 THR cc_start: 0.7729 (m) cc_final: 0.7146 (m) REVERT: D 1196 LEU cc_start: 0.8336 (mm) cc_final: 0.7626 (tp) REVERT: D 1199 PHE cc_start: 0.7078 (m-10) cc_final: 0.6749 (m-10) REVERT: D 1363 TYR cc_start: 0.8077 (t80) cc_final: 0.7702 (t80) REVERT: E 18 ASP cc_start: 0.7163 (p0) cc_final: 0.6812 (p0) REVERT: E 44 ASP cc_start: 0.8294 (m-30) cc_final: 0.8026 (m-30) REVERT: F 20 LYS cc_start: 0.8543 (mttp) cc_final: 0.8007 (tptt) REVERT: F 77 ILE cc_start: 0.8983 (mt) cc_final: 0.8564 (tp) REVERT: F 175 PHE cc_start: 0.8768 (t80) cc_final: 0.8433 (t80) outliers start: 1 outliers final: 0 residues processed: 402 average time/residue: 0.3682 time to fit residues: 241.4461 Evaluate side-chains 309 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 3.197 ------------------------------------------------------------------------------- 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: 7.9990 chunk 130 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 98 optimal weight: 0.0270 chunk 64 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 overall best weight: 5.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN B 147 GLN C 343 HIS C 649 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1299 ASN D 164 GLN D 340 GLN D 739 GLN D 979 ASN ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 HIS ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 28790 Z= 0.391 Angle : 0.665 12.399 39328 Z= 0.347 Chirality : 0.046 0.195 4506 Planarity : 0.005 0.084 4793 Dihedral : 16.600 178.333 4798 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.04 % Allowed : 1.56 % Favored : 98.41 % 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: -1.05 (0.14), residues: 3325 helix: 0.96 (0.16), residues: 1153 sheet: -0.77 (0.25), residues: 429 loop : -1.90 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D1193 HIS 0.007 0.001 HIS C1313 PHE 0.034 0.002 PHE C 514 TYR 0.023 0.002 TYR C 395 ARG 0.007 0.001 ARG C 180 *********************** 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 388 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 387 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8068 (t0) cc_final: 0.7790 (t0) REVERT: B 51 MET cc_start: 0.8338 (mmm) cc_final: 0.7952 (mmm) REVERT: B 93 GLN cc_start: 0.8238 (pm20) cc_final: 0.8010 (pm20) REVERT: C 132 ASP cc_start: 0.7847 (t0) cc_final: 0.7566 (t0) REVERT: C 195 PHE cc_start: 0.7560 (m-80) cc_final: 0.6975 (m-80) REVERT: C 347 ILE cc_start: 0.8624 (mm) cc_final: 0.8030 (mm) REVERT: C 515 MET cc_start: 0.8642 (ptt) cc_final: 0.8434 (ptp) REVERT: C 524 ILE cc_start: 0.9163 (tt) cc_final: 0.8953 (tt) REVERT: C 685 MET cc_start: 0.8674 (mtm) cc_final: 0.8397 (mtm) REVERT: C 739 ASP cc_start: 0.8440 (p0) cc_final: 0.8162 (p0) REVERT: C 785 ASP cc_start: 0.7896 (m-30) cc_final: 0.7085 (p0) REVERT: C 1018 TYR cc_start: 0.7743 (t80) cc_final: 0.7093 (t80) REVERT: C 1274 GLU cc_start: 0.7835 (mp0) cc_final: 0.7455 (mp0) REVERT: C 1319 MET cc_start: 0.8883 (tpp) cc_final: 0.8520 (ttp) REVERT: D 457 TYR cc_start: 0.8739 (m-80) cc_final: 0.8463 (m-80) REVERT: D 527 LEU cc_start: 0.8948 (mm) cc_final: 0.8745 (mm) REVERT: D 532 GLU cc_start: 0.8431 (tp30) cc_final: 0.7860 (tp30) REVERT: D 1196 LEU cc_start: 0.8579 (mm) cc_final: 0.8201 (tp) REVERT: D 1199 PHE cc_start: 0.7276 (m-10) cc_final: 0.6824 (m-10) REVERT: D 1363 TYR cc_start: 0.8377 (t80) cc_final: 0.7922 (t80) REVERT: E 15 ASN cc_start: 0.8385 (t0) cc_final: 0.7967 (t0) REVERT: E 18 ASP cc_start: 0.7389 (p0) cc_final: 0.7031 (p0) REVERT: F 20 LYS cc_start: 0.8647 (mttp) cc_final: 0.8041 (tptt) REVERT: F 67 ASP cc_start: 0.7718 (m-30) cc_final: 0.7448 (t0) REVERT: F 77 ILE cc_start: 0.9010 (mt) cc_final: 0.8644 (tp) outliers start: 1 outliers final: 0 residues processed: 387 average time/residue: 0.3981 time to fit residues: 250.4440 Evaluate side-chains 299 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 3.481 ------------------------------------------------------------------------------- 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: 3.9990 chunk 313 optimal weight: 20.0000 chunk 285 optimal weight: 3.9990 chunk 304 optimal weight: 0.6980 chunk 312 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 132 optimal weight: 0.3980 chunk 239 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 275 optimal weight: 50.0000 chunk 287 optimal weight: 0.4980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 649 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN C1299 ASN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 HIS ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28790 Z= 0.198 Angle : 0.562 12.265 39328 Z= 0.294 Chirality : 0.042 0.207 4506 Planarity : 0.004 0.088 4793 Dihedral : 16.494 179.050 4798 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.07 % Allowed : 0.60 % Favored : 99.33 % 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: -0.77 (0.14), residues: 3325 helix: 1.23 (0.16), residues: 1157 sheet: -0.63 (0.27), residues: 403 loop : -1.75 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D1193 HIS 0.004 0.001 HIS D 430 PHE 0.023 0.001 PHE C 186 TYR 0.018 0.001 TYR C 395 ARG 0.007 0.000 ARG C 180 *********************** 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 384 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 382 time to evaluate : 3.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8122 (t0) cc_final: 0.7807 (t0) REVERT: B 51 MET cc_start: 0.8226 (mmm) cc_final: 0.7955 (mmm) REVERT: C 132 ASP cc_start: 0.7855 (t0) cc_final: 0.7554 (t0) REVERT: C 195 PHE cc_start: 0.7305 (m-80) cc_final: 0.6788 (m-80) REVERT: C 347 ILE cc_start: 0.8599 (mm) cc_final: 0.8074 (mm) REVERT: C 370 MET cc_start: 0.8174 (mmp) cc_final: 0.7899 (mmm) REVERT: C 441 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7146 (mp0) REVERT: C 524 ILE cc_start: 0.9119 (tt) cc_final: 0.8918 (tt) REVERT: C 704 MET cc_start: 0.8218 (mmm) cc_final: 0.8005 (mmp) REVERT: C 739 ASP cc_start: 0.8327 (p0) cc_final: 0.8062 (p0) REVERT: C 785 ASP cc_start: 0.7863 (m-30) cc_final: 0.6924 (p0) REVERT: C 1274 GLU cc_start: 0.7837 (mp0) cc_final: 0.7518 (mp0) REVERT: C 1319 MET cc_start: 0.8840 (tpp) cc_final: 0.8393 (ttp) REVERT: D 330 MET cc_start: 0.7822 (ttm) cc_final: 0.7414 (ttm) REVERT: D 485 MET cc_start: 0.8828 (ttm) cc_final: 0.8557 (ttt) REVERT: D 527 LEU cc_start: 0.8987 (mm) cc_final: 0.8701 (mm) REVERT: D 532 GLU cc_start: 0.8401 (tp30) cc_final: 0.8050 (mm-30) REVERT: D 697 MET cc_start: 0.8152 (ttp) cc_final: 0.7943 (tpp) REVERT: D 1196 LEU cc_start: 0.8512 (mm) cc_final: 0.7835 (tp) REVERT: D 1199 PHE cc_start: 0.7402 (m-10) cc_final: 0.7184 (m-10) REVERT: D 1363 TYR cc_start: 0.8138 (t80) cc_final: 0.7677 (t80) REVERT: E 15 ASN cc_start: 0.8340 (t0) cc_final: 0.7999 (t0) REVERT: E 18 ASP cc_start: 0.7314 (p0) cc_final: 0.6952 (p0) REVERT: E 44 ASP cc_start: 0.8323 (m-30) cc_final: 0.8011 (m-30) REVERT: F 20 LYS cc_start: 0.8601 (mttp) cc_final: 0.8059 (tptt) REVERT: F 67 ASP cc_start: 0.7621 (m-30) cc_final: 0.7354 (t0) REVERT: F 77 ILE cc_start: 0.8951 (mt) cc_final: 0.8588 (tp) REVERT: F 175 PHE cc_start: 0.8801 (t80) cc_final: 0.8438 (t80) outliers start: 2 outliers final: 0 residues processed: 383 average time/residue: 0.3737 time to fit residues: 233.4324 Evaluate side-chains 305 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 3.212 ------------------------------------------------------------------------------- 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: 0.2980 chunk 199 optimal weight: 5.9990 chunk 321 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 337 optimal weight: 10.0000 chunk 310 optimal weight: 0.7980 chunk 268 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 649 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN C1209 GLN C1288 GLN C1299 ASN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1366 HIS ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4563 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= 0.158 Angle : 0.539 11.653 39328 Z= 0.281 Chirality : 0.041 0.190 4506 Planarity : 0.004 0.084 4793 Dihedral : 16.417 177.989 4798 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.07 % Allowed : 0.28 % Favored : 99.65 % 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: -0.58 (0.15), residues: 3325 helix: 1.42 (0.16), residues: 1155 sheet: -0.48 (0.27), residues: 393 loop : -1.66 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D1193 HIS 0.003 0.000 HIS A 37 PHE 0.024 0.001 PHE C 186 TYR 0.033 0.001 TYR D1186 ARG 0.005 0.000 ARG C 97 ********************** 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 384 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 382 time to evaluate : 3.110 Fit side-chains revert: symmetry clash REVERT: A 84 ASN cc_start: 0.7965 (t0) cc_final: 0.7703 (t0) REVERT: C 132 ASP cc_start: 0.7862 (t0) cc_final: 0.7544 (t0) REVERT: C 195 PHE cc_start: 0.7154 (m-80) cc_final: 0.6655 (m-80) REVERT: C 347 ILE cc_start: 0.8573 (mm) cc_final: 0.8065 (mm) REVERT: C 370 MET cc_start: 0.8187 (mmp) cc_final: 0.7887 (mmm) REVERT: C 441 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7118 (mp0) REVERT: C 524 ILE cc_start: 0.9046 (tt) cc_final: 0.8798 (tt) REVERT: C 711 ASP cc_start: 0.7538 (m-30) cc_final: 0.7059 (m-30) REVERT: C 739 ASP cc_start: 0.8313 (p0) cc_final: 0.8063 (p0) REVERT: C 785 ASP cc_start: 0.7902 (m-30) cc_final: 0.7043 (p0) REVERT: C 805 MET cc_start: 0.7991 (ptm) cc_final: 0.7764 (ptm) REVERT: C 1010 GLN cc_start: 0.7693 (pm20) cc_final: 0.7485 (pm20) REVERT: C 1273 MET cc_start: 0.8350 (mtt) cc_final: 0.8038 (mtm) REVERT: C 1274 GLU cc_start: 0.7851 (mp0) cc_final: 0.7516 (mp0) REVERT: C 1304 MET cc_start: 0.8495 (tpp) cc_final: 0.8094 (ttm) REVERT: C 1319 MET cc_start: 0.8826 (tpp) cc_final: 0.8311 (ttp) REVERT: D 114 ILE cc_start: 0.9337 (tp) cc_final: 0.9120 (tp) REVERT: D 527 LEU cc_start: 0.8918 (mm) cc_final: 0.8648 (mm) REVERT: D 532 GLU cc_start: 0.8321 (tp30) cc_final: 0.7969 (mm-30) REVERT: D 1196 LEU cc_start: 0.8429 (mm) cc_final: 0.7802 (tp) REVERT: D 1307 LEU cc_start: 0.9100 (pt) cc_final: 0.8570 (mt) REVERT: D 1327 GLU cc_start: 0.8228 (tt0) cc_final: 0.8014 (tt0) REVERT: D 1363 TYR cc_start: 0.8049 (t80) cc_final: 0.7625 (t80) REVERT: E 15 ASN cc_start: 0.8289 (t0) cc_final: 0.7971 (t0) REVERT: E 18 ASP cc_start: 0.7221 (p0) cc_final: 0.6914 (p0) REVERT: F 20 LYS cc_start: 0.8562 (mttp) cc_final: 0.8045 (tptt) REVERT: F 23 ASN cc_start: 0.8356 (p0) cc_final: 0.8128 (m-40) REVERT: F 67 ASP cc_start: 0.7482 (m-30) cc_final: 0.7281 (t0) REVERT: F 77 ILE cc_start: 0.8938 (mt) cc_final: 0.8523 (tp) REVERT: F 175 PHE cc_start: 0.8782 (t80) cc_final: 0.8381 (t80) outliers start: 2 outliers final: 1 residues processed: 383 average time/residue: 0.3762 time to fit residues: 235.0243 Evaluate side-chains 317 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 3.216 ------------------------------------------------------------------------------- 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: 0.5980 chunk 213 optimal weight: 0.7980 chunk 286 optimal weight: 30.0000 chunk 82 optimal weight: 10.0000 chunk 247 optimal weight: 0.3980 chunk 39 optimal weight: 0.0770 chunk 74 optimal weight: 7.9990 chunk 269 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 276 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 649 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 GLN C 799 ASN C1209 GLN C1288 GLN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.146666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.119682 restraints weight = 47592.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118482 restraints weight = 59016.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119441 restraints weight = 64975.571| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28790 Z= 0.164 Angle : 0.544 11.937 39328 Z= 0.282 Chirality : 0.041 0.226 4506 Planarity : 0.004 0.082 4793 Dihedral : 16.376 178.900 4798 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.65 % 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: -0.52 (0.15), residues: 3325 helix: 1.47 (0.16), residues: 1155 sheet: -0.46 (0.28), residues: 389 loop : -1.63 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D1193 HIS 0.003 0.000 HIS D 450 PHE 0.024 0.001 PHE C 186 TYR 0.036 0.001 TYR D1186 ARG 0.004 0.000 ARG D 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5769.81 seconds wall clock time: 106 minutes 54.27 seconds (6414.27 seconds total)