Starting phenix.real_space_refine on Thu Feb 22 05:31:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vba_31876/02_2024/7vba_31876_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vba_31876/02_2024/7vba_31876.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vba_31876/02_2024/7vba_31876_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vba_31876/02_2024/7vba_31876_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vba_31876/02_2024/7vba_31876_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vba_31876/02_2024/7vba_31876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vba_31876/02_2024/7vba_31876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vba_31876/02_2024/7vba_31876_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vba_31876/02_2024/7vba_31876_neut_trim_updated.pdb" } resolution = 2.89 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= -0.002 sd= 0.151 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 5 6.06 5 P 44 5.49 5 Mg 1 5.21 5 S 220 5.16 5 C 20865 2.51 5 N 5767 2.21 5 O 6177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A ARG 722": "NH1" <-> "NH2" Residue "A ARG 793": "NH1" <-> "NH2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A GLU 867": "OE1" <-> "OE2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A GLU 1021": "OE1" <-> "OE2" Residue "A GLU 1055": "OE1" <-> "OE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A GLU 1098": "OE1" <-> "OE2" Residue "A GLU 1106": "OE1" <-> "OE2" Residue "A ARG 1110": "NH1" <-> "NH2" Residue "A ARG 1122": "NH1" <-> "NH2" Residue "A GLU 1130": "OE1" <-> "OE2" Residue "A ARG 1133": "NH1" <-> "NH2" Residue "A GLU 1164": "OE1" <-> "OE2" Residue "A GLU 1183": "OE1" <-> "OE2" Residue "A GLU 1292": "OE1" <-> "OE2" Residue "A GLU 1330": "OE1" <-> "OE2" Residue "A ARG 1340": "NH1" <-> "NH2" Residue "A GLU 1352": "OE1" <-> "OE2" Residue "A ARG 1500": "NH1" <-> "NH2" Residue "A GLU 1521": "OE1" <-> "OE2" Residue "A GLU 1575": "OE1" <-> "OE2" Residue "A GLU 1622": "OE1" <-> "OE2" Residue "A GLU 1624": "OE1" <-> "OE2" Residue "A GLU 1675": "OE1" <-> "OE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B GLU 638": "OE1" <-> "OE2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 754": "OE1" <-> "OE2" Residue "B GLU 835": "OE1" <-> "OE2" Residue "B GLU 845": "OE1" <-> "OE2" Residue "B GLU 955": "OE1" <-> "OE2" Residue "B GLU 964": "OE1" <-> "OE2" Residue "B GLU 987": "OE1" <-> "OE2" Residue "B GLU 989": "OE1" <-> "OE2" Residue "B PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1029": "NH1" <-> "NH2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C ARG 298": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 141": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "N GLU 33": "OE1" <-> "OE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N GLU 100": "OE1" <-> "OE2" Residue "N GLU 119": "OE1" <-> "OE2" Residue "N ARG 148": "NH1" <-> "NH2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "M GLU 100": "OE1" <-> "OE2" Residue "M GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33079 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1473, 11749 Classifications: {'peptide': 1473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 71, 'TRANS': 1401} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 8912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 8912 Classifications: {'peptide': 1123} Link IDs: {'PTRANS': 63, 'TRANS': 1059} Chain breaks: 1 Chain: "C" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2697 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain: "E" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1641 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 10, 'TRANS': 188} Chain breaks: 1 Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "H" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1176 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "I" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 447 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 863 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 379 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "N" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1105 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 24, 'TRANS': 126} Chain: "G" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1229 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "M" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 867 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "R" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 5} Link IDs: {'rna3p': 7} Chain: "T" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 456 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "U" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 238 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' MG': 1, ' ZN': 2, '2TM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 455 SG CYS A 64 60.563 56.328 58.882 1.00 70.96 S ATOM 474 SG CYS A 67 63.144 55.957 56.706 1.00 70.13 S ATOM 529 SG CYS A 74 62.920 57.836 60.489 1.00 63.65 S ATOM 767 SG CYS A 104 63.181 108.926 50.085 1.00 76.34 S ATOM 789 SG CYS A 107 64.340 109.379 46.745 1.00 82.67 S ATOM 1491 SG CYS A 205 66.268 111.265 49.614 1.00 87.17 S ATOM 20214 SG CYS B1070 75.151 66.247 49.271 1.00 51.70 S ATOM 20236 SG CYS B1073 73.880 69.240 48.145 1.00 54.67 S ATOM 20370 SG CYS B1098 71.599 66.222 48.929 1.00 72.84 S ATOM 20391 SG CYS B1101 73.406 66.995 45.360 1.00 83.89 S ATOM 27287 SG CYS J 7 77.049 45.364 128.555 1.00 34.15 S ATOM 27311 SG CYS J 10 79.902 42.644 130.073 1.00 21.98 S ATOM 27575 SG CYS J 44 80.106 46.624 130.501 1.00 21.89 S ATOM 27581 SG CYS J 45 78.026 44.410 132.565 1.00 24.31 S ATOM 28651 SG CYS L 19 35.893 46.649 111.648 1.00 40.38 S ATOM 28787 SG CYS L 36 33.517 44.676 110.069 1.00 44.67 S ATOM 28813 SG CYS L 39 32.454 47.099 111.952 1.00 47.99 S Residues with excluded nonbonded symmetry interactions: 161 residue: pdb=" N GLY N 127 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 127 " occ=0.00 residue: pdb=" N GLY N 144 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 144 " occ=0.00 residue: pdb=" N GLY N 153 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 153 " occ=0.00 residue: pdb=" N GLY N 154 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 154 " occ=0.00 residue: pdb=" N SER G 46 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER G 46 " occ=0.00 residue: pdb=" N CYS G 47 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS G 47 " occ=0.00 residue: pdb=" N LEU G 48 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU G 48 " occ=0.00 residue: pdb=" N VAL G 49 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL G 49 " occ=0.00 residue: pdb=" N ALA G 50 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 50 " occ=0.00 residue: pdb=" N GLY G 51 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY G 51 " occ=0.00 residue: pdb=" N PRO G 52 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO G 52 " occ=0.00 residue: pdb=" N HIS G 53 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS G 53 " occ=0.00 ... (remaining 149 not shown) Time building chain proxies: 16.72, per 1000 atoms: 0.51 Number of scatterers: 33079 At special positions: 0 Unit cell: (155.992, 161.262, 177.072, 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 5 29.99 S 220 16.00 P 44 15.00 Mg 1 11.99 O 6177 8.00 N 5767 7.00 C 20865 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: 12.21 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 64 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 205 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 107 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 104 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1101 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1073 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1070 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 44 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 7 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 39 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 36 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 19 " Number of angles added : 12 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 125 helices and 33 sheets defined 28.2% alpha, 11.6% beta 11 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 15.28 Creating SS restraints... Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'A' and resid 114 through 129 removed outlier: 4.222A pdb=" N VAL A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 158 through 171 removed outlier: 4.260A pdb=" N TYR A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 258 through 279 removed outlier: 3.700A pdb=" N LYS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 297 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 323 through 347 Processing helix chain 'A' and resid 382 through 400 Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.595A pdb=" N CYS A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS A 583 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A 584 " --> pdb=" O ASN A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 610 Processing helix chain 'A' and resid 632 through 641 removed outlier: 4.211A pdb=" N VAL A 636 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER A 637 " --> pdb=" O HIS A 634 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY A 638 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 639 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET A 641 " --> pdb=" O GLY A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 653 No H-bonds generated for 'chain 'A' and resid 650 through 653' Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.810A pdb=" N ASN A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 732 removed outlier: 3.654A pdb=" N MET A 732 " --> pdb=" O PRO A 729 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 729 through 732' Processing helix chain 'A' and resid 761 through 769 Processing helix chain 'A' and resid 771 through 791 removed outlier: 3.543A pdb=" N LEU A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 821 removed outlier: 3.608A pdb=" N THR A 820 " --> pdb=" O ILE A 816 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N HIS A 821 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 830 Processing helix chain 'A' and resid 841 through 850 Processing helix chain 'A' and resid 856 through 880 removed outlier: 3.713A pdb=" N MET A 860 " --> pdb=" O ARG A 856 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 861 " --> pdb=" O ASP A 857 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 868 " --> pdb=" O LYS A 864 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 909 No H-bonds generated for 'chain 'A' and resid 906 through 909' Processing helix chain 'A' and resid 945 through 948 Processing helix chain 'A' and resid 961 through 995 removed outlier: 3.655A pdb=" N LEU A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1029 Processing helix chain 'A' and resid 1037 through 1042 Processing helix chain 'A' and resid 1044 through 1050 Processing helix chain 'A' and resid 1053 through 1059 removed outlier: 3.609A pdb=" N LEU A1057 " --> pdb=" O LEU A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1078 Processing helix chain 'A' and resid 1088 through 1091 No H-bonds generated for 'chain 'A' and resid 1088 through 1091' Processing helix chain 'A' and resid 1096 through 1102 removed outlier: 4.499A pdb=" N ALA A1102 " --> pdb=" O GLU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1125 removed outlier: 4.199A pdb=" N GLU A1119 " --> pdb=" O PRO A1115 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1139 No H-bonds generated for 'chain 'A' and resid 1137 through 1139' Processing helix chain 'A' and resid 1146 through 1149 No H-bonds generated for 'chain 'A' and resid 1146 through 1149' Processing helix chain 'A' and resid 1161 through 1178 removed outlier: 3.800A pdb=" N THR A1165 " --> pdb=" O GLU A1161 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A1176 " --> pdb=" O GLN A1172 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1201 removed outlier: 3.949A pdb=" N THR A1194 " --> pdb=" O ASP A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1225 Proline residue: A1222 - end of helix Processing helix chain 'A' and resid 1245 through 1251 Processing helix chain 'A' and resid 1272 through 1285 removed outlier: 3.925A pdb=" N LYS A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A1280 " --> pdb=" O LYS A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1292 No H-bonds generated for 'chain 'A' and resid 1290 through 1292' Processing helix chain 'A' and resid 1324 through 1326 No H-bonds generated for 'chain 'A' and resid 1324 through 1326' Processing helix chain 'A' and resid 1328 through 1330 No H-bonds generated for 'chain 'A' and resid 1328 through 1330' Processing helix chain 'A' and resid 1335 through 1344 Processing helix chain 'A' and resid 1346 through 1358 removed outlier: 4.116A pdb=" N MET A1351 " --> pdb=" O PHE A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1508 removed outlier: 3.640A pdb=" N ARG A1501 " --> pdb=" O ALA A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1546 Processing helix chain 'A' and resid 1586 through 1591 removed outlier: 4.967A pdb=" N LYS A1590 " --> pdb=" O GLU A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1611 No H-bonds generated for 'chain 'A' and resid 1608 through 1611' Processing helix chain 'A' and resid 1614 through 1632 removed outlier: 4.247A pdb=" N ARG A1619 " --> pdb=" O GLU A1615 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1620 " --> pdb=" O ALA A1616 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A1631 " --> pdb=" O ASP A1627 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR A1632 " --> pdb=" O VAL A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1648 removed outlier: 3.602A pdb=" N LEU A1643 " --> pdb=" O ARG A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1677 through 1686 Processing helix chain 'A' and resid 1696 through 1701 Processing helix chain 'B' and resid 40 through 60 removed outlier: 3.581A pdb=" N SER B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 46 " --> pdb=" O HIS B 42 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 No H-bonds generated for 'chain 'B' and resid 155 through 158' Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.678A pdb=" N LYS B 199 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR B 200 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 261 through 268 Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 297 through 312 removed outlier: 4.701A pdb=" N VAL B 310 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS B 311 " --> pdb=" O CYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 377 through 403 removed outlier: 3.635A pdb=" N GLU B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 removed outlier: 5.233A pdb=" N THR B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 422 removed outlier: 3.666A pdb=" N THR B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 removed outlier: 4.092A pdb=" N PHE B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 431 " --> pdb=" O THR B 427 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 467 removed outlier: 3.947A pdb=" N SER B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 479 No H-bonds generated for 'chain 'B' and resid 477 through 479' Processing helix chain 'B' and resid 530 through 537 removed outlier: 3.653A pdb=" N CYS B 535 " --> pdb=" O PRO B 531 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 584 Processing helix chain 'B' and resid 638 through 641 removed outlier: 3.843A pdb=" N PHE B 641 " --> pdb=" O GLU B 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 641' Processing helix chain 'B' and resid 677 through 679 No H-bonds generated for 'chain 'B' and resid 677 through 679' Processing helix chain 'B' and resid 682 through 691 removed outlier: 3.564A pdb=" N TYR B 687 " --> pdb=" O PRO B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 801 through 803 No H-bonds generated for 'chain 'B' and resid 801 through 803' Processing helix chain 'B' and resid 920 through 923 No H-bonds generated for 'chain 'B' and resid 920 through 923' Processing helix chain 'B' and resid 926 through 941 removed outlier: 3.820A pdb=" N MET B 933 " --> pdb=" O LEU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 969 removed outlier: 3.503A pdb=" N ALA B 969 " --> pdb=" O MET B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1045 Processing helix chain 'B' and resid 1051 through 1058 Processing helix chain 'B' and resid 1114 through 1126 removed outlier: 3.764A pdb=" N MET B1126 " --> pdb=" O GLU B1122 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 318 through 340 Processing helix chain 'E' and resid 5 through 23 Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 43 Processing helix chain 'E' and resid 84 through 97 removed outlier: 3.718A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 120 removed outlier: 4.228A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 162 removed outlier: 3.845A pdb=" N THR E 157 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 75 Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'H' and resid 129 through 131 No H-bonds generated for 'chain 'H' and resid 129 through 131' Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 31 through 37 Processing helix chain 'J' and resid 43 through 50 removed outlier: 3.755A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 59 No H-bonds generated for 'chain 'J' and resid 56 through 59' Processing helix chain 'K' and resid 49 through 59 Processing helix chain 'K' and resid 94 through 127 removed outlier: 3.658A pdb=" N ASN K 101 " --> pdb=" O GLN K 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 35 No H-bonds generated for 'chain 'N' and resid 32 through 35' Processing helix chain 'N' and resid 53 through 56 Processing helix chain 'N' and resid 99 through 101 No H-bonds generated for 'chain 'N' and resid 99 through 101' Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'G' and resid 67 through 73 removed outlier: 3.801A pdb=" N ARG G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 159 No H-bonds generated for 'chain 'G' and resid 157 through 159' Processing helix chain 'M' and resid 36 through 38 No H-bonds generated for 'chain 'M' and resid 36 through 38' Processing helix chain 'M' and resid 80 through 82 No H-bonds generated for 'chain 'M' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'A' and resid 79 through 82 Processing sheet with id= B, first strand: chain 'A' and resid 440 through 443 Processing sheet with id= C, first strand: chain 'A' and resid 445 through 447 removed outlier: 6.247A pdb=" N LEU A 575 " --> pdb=" O CYS A 446 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 467 through 471 removed outlier: 4.137A pdb=" N MET A 496 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS A 541 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA A 494 " --> pdb=" O HIS A 541 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 705 through 708 Processing sheet with id= F, first strand: chain 'A' and resid 1264 through 1267 removed outlier: 3.845A pdb=" N VAL A1266 " --> pdb=" O LEU A1578 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A1577 " --> pdb=" O ASN A1565 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1298 through 1300 Processing sheet with id= H, first strand: chain 'B' and resid 64 through 68 removed outlier: 3.530A pdb=" N PHE B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP B 117 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA B 80 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 115 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 82 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS B 113 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 116 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE B 133 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 118 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS B 131 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TRP B 120 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE B 129 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 122 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS B 127 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 182 through 184 removed outlier: 3.506A pdb=" N LEU B 182 " --> pdb=" O LEU B 375 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 190 through 193 removed outlier: 6.018A pdb=" N ASN B 223 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE B 239 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 471 through 473 Processing sheet with id= L, first strand: chain 'B' and resid 518 through 520 Processing sheet with id= M, first strand: chain 'B' and resid 594 through 598 Processing sheet with id= N, first strand: chain 'B' and resid 712 through 714 removed outlier: 4.669A pdb=" N CYS B 866 " --> pdb=" O CYS B 855 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN B 851 " --> pdb=" O THR B 870 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG B 872 " --> pdb=" O VAL B 849 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL B 849 " --> pdb=" O ARG B 872 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 893 through 897 removed outlier: 7.461A pdb=" N MET B 757 " --> pdb=" O SER B 894 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 896 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 759 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE B 993 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 828 through 830 removed outlier: 3.516A pdb=" N TYR B 828 " --> pdb=" O PHE B 837 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 835 " --> pdb=" O ASN B 830 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 1068 through 1070 Processing sheet with id= R, first strand: chain 'C' and resid 173 through 176 removed outlier: 4.560A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 233 through 235 Processing sheet with id= T, first strand: chain 'C' and resid 237 through 241 Processing sheet with id= U, first strand: chain 'C' and resid 262 through 265 Processing sheet with id= V, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.340A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.561A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= Y, first strand: chain 'H' and resid 25 through 31 removed outlier: 3.810A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 27 through 31 Processing sheet with id= AA, first strand: chain 'L' and resid 25 through 27 Processing sheet with id= AB, first strand: chain 'N' and resid 43 through 46 removed outlier: 6.721A pdb=" N GLY N 113 " --> pdb=" O LEU N 44 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLN N 46 " --> pdb=" O GLY N 113 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU N 115 " --> pdb=" O GLN N 46 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR N 114 " --> pdb=" O SER N 85 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY N 65 " --> pdb=" O SER N 84 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'N' and resid 95 through 97 Processing sheet with id= AD, first strand: chain 'G' and resid 48 through 59 Processing sheet with id= AE, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.560A pdb=" N GLN M 98 " --> pdb=" O ASN M 93 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS M 87 " --> pdb=" O ALA M 104 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'M' and resid 23 through 28 Processing sheet with id= AG, first strand: chain 'M' and resid 40 through 45 871 hydrogen bonds defined for protein. 2484 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 13.02 Time building geometry restraints manager: 13.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5404 1.29 - 1.43: 8775 1.43 - 1.56: 19250 1.56 - 1.70: 83 1.70 - 1.84: 343 Bond restraints: 33855 Sorted by residual: bond pdb=" C1' 2TM A2004 " pdb=" C2' 2TM A2004 " ideal model delta sigma weight residual 1.327 1.533 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C1' 2TM A2004 " pdb=" O4' 2TM A2004 " ideal model delta sigma weight residual 1.609 1.410 0.199 2.00e-02 2.50e+03 9.92e+01 bond pdb=" C ARG M 66 " pdb=" N LEU M 67 " ideal model delta sigma weight residual 1.331 1.221 0.110 1.22e-02 6.72e+03 8.09e+01 bond pdb=" C PRO B 590 " pdb=" O PRO B 590 " ideal model delta sigma weight residual 1.246 1.176 0.070 8.50e-03 1.38e+04 6.78e+01 bond pdb=" C4' 2TM A2004 " pdb=" O4' 2TM A2004 " ideal model delta sigma weight residual 1.287 1.447 -0.160 2.00e-02 2.50e+03 6.42e+01 ... (remaining 33850 not shown) Histogram of bond angle deviations from ideal: 95.31 - 103.19: 586 103.19 - 111.08: 12688 111.08 - 118.97: 15540 118.97 - 126.85: 16687 126.85 - 134.74: 446 Bond angle restraints: 45947 Sorted by residual: angle pdb=" N VAL C 164 " pdb=" CA VAL C 164 " pdb=" C VAL C 164 " ideal model delta sigma weight residual 112.12 98.66 13.46 8.40e-01 1.42e+00 2.57e+02 angle pdb=" N GLU A1507 " pdb=" CA GLU A1507 " pdb=" C GLU A1507 " ideal model delta sigma weight residual 111.07 99.33 11.74 1.07e+00 8.73e-01 1.20e+02 angle pdb=" N THR K 25 " pdb=" CA THR K 25 " pdb=" C THR K 25 " ideal model delta sigma weight residual 113.18 100.87 12.31 1.21e+00 6.83e-01 1.03e+02 angle pdb=" N LEU B 19 " pdb=" CA LEU B 19 " pdb=" C LEU B 19 " ideal model delta sigma weight residual 110.53 97.54 12.99 1.32e+00 5.74e-01 9.68e+01 angle pdb=" N HIS B 159 " pdb=" CA HIS B 159 " pdb=" C HIS B 159 " ideal model delta sigma weight residual 110.32 95.31 15.01 1.59e+00 3.96e-01 8.91e+01 ... (remaining 45942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 18027 18.03 - 36.05: 1814 36.05 - 54.08: 506 54.08 - 72.11: 127 72.11 - 90.14: 34 Dihedral angle restraints: 20508 sinusoidal: 8762 harmonic: 11746 Sorted by residual: dihedral pdb=" N GLN A 553 " pdb=" C GLN A 553 " pdb=" CA GLN A 553 " pdb=" CB GLN A 553 " ideal model delta harmonic sigma weight residual 122.80 150.82 -28.02 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" C GLN A 553 " pdb=" N GLN A 553 " pdb=" CA GLN A 553 " pdb=" CB GLN A 553 " ideal model delta harmonic sigma weight residual -122.60 -150.36 27.76 0 2.50e+00 1.60e-01 1.23e+02 dihedral pdb=" C TYR B 730 " pdb=" N TYR B 730 " pdb=" CA TYR B 730 " pdb=" CB TYR B 730 " ideal model delta harmonic sigma weight residual -122.60 -104.21 -18.39 0 2.50e+00 1.60e-01 5.41e+01 ... (remaining 20505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 4908 0.249 - 0.499: 174 0.499 - 0.748: 10 0.748 - 0.997: 0 0.997 - 1.246: 1 Chirality restraints: 5093 Sorted by residual: chirality pdb=" CA GLN A 553 " pdb=" N GLN A 553 " pdb=" C GLN A 553 " pdb=" CB GLN A 553 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.88e+01 chirality pdb=" CA PRO C 259 " pdb=" N PRO C 259 " pdb=" C PRO C 259 " pdb=" CB PRO C 259 " both_signs ideal model delta sigma weight residual False 2.72 1.98 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CB THR K 25 " pdb=" CA THR K 25 " pdb=" OG1 THR K 25 " pdb=" CG2 THR K 25 " both_signs ideal model delta sigma weight residual False 2.55 1.89 0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 5090 not shown) Planarity restraints: 5797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET M 109 " 0.029 2.00e-02 2.50e+03 5.97e-02 3.56e+01 pdb=" C MET M 109 " -0.103 2.00e-02 2.50e+03 pdb=" O MET M 109 " 0.041 2.00e-02 2.50e+03 pdb=" N GLN M 110 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 14 " 0.027 2.00e-02 2.50e+03 5.33e-02 2.84e+01 pdb=" C ASP H 14 " -0.092 2.00e-02 2.50e+03 pdb=" O ASP H 14 " 0.034 2.00e-02 2.50e+03 pdb=" N ILE H 15 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY N 104 " -0.026 2.00e-02 2.50e+03 5.16e-02 2.67e+01 pdb=" C GLY N 104 " 0.089 2.00e-02 2.50e+03 pdb=" O GLY N 104 " -0.034 2.00e-02 2.50e+03 pdb=" N LEU N 105 " -0.029 2.00e-02 2.50e+03 ... (remaining 5794 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 72 2.39 - 3.02: 19569 3.02 - 3.64: 47119 3.64 - 4.27: 77707 4.27 - 4.90: 130015 Nonbonded interactions: 274482 Sorted by model distance: nonbonded pdb=" O ASP I 16 " pdb=" CD2 LEU M 67 " model vdw 1.758 3.460 nonbonded pdb=" OD1 ASP A 590 " pdb="MG MG A2003 " model vdw 1.982 2.170 nonbonded pdb=" OE1 GLN M 12 " pdb=" NE2 GLN M 98 " model vdw 2.007 2.520 nonbonded pdb=" O3' U R -1 " pdb="MG MG A2003 " model vdw 2.053 2.170 nonbonded pdb=" NZ LYS A 408 " pdb=" CD2 LEU A 409 " model vdw 2.055 3.540 ... (remaining 274477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.030 Extract box with map and model: 8.650 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 97.920 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.010 0.206 33855 Z= 0.635 Angle : 1.434 16.650 45947 Z= 1.005 Chirality : 0.099 1.246 5093 Planarity : 0.008 0.117 5797 Dihedral : 16.309 90.136 12932 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 27.84 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.65 % Favored : 91.00 % Rotamer: Outliers : 5.76 % Allowed : 7.20 % Favored : 87.04 % Cbeta Deviations : 2.11 % Peptide Plane: Cis-proline : 0.00 % 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: -3.50 (0.12), residues: 4001 helix: -1.95 (0.13), residues: 1212 sheet: -1.90 (0.19), residues: 646 loop : -2.74 (0.12), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 9 HIS 0.021 0.002 HIS C 166 PHE 0.050 0.002 PHE B 75 TYR 0.046 0.002 TYR B 826 ARG 0.010 0.001 ARG G 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 691 time to evaluate : 3.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7413 (mtmt) cc_final: 0.7048 (mttm) REVERT: A 91 LEU cc_start: 0.7675 (pt) cc_final: 0.6947 (pt) REVERT: A 172 ASN cc_start: 0.8099 (t0) cc_final: 0.7872 (t0) REVERT: A 200 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8772 (mmp) REVERT: A 204 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6578 (mpp80) REVERT: A 292 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6161 (m-80) REVERT: A 381 GLN cc_start: 0.4624 (OUTLIER) cc_final: 0.3979 (tt0) REVERT: A 407 ASP cc_start: 0.6407 (t0) cc_final: 0.6009 (t70) REVERT: A 411 MET cc_start: 0.7187 (mpp) cc_final: 0.6842 (mpt) REVERT: A 454 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7987 (p0) REVERT: A 465 LYS cc_start: 0.8509 (tttm) cc_final: 0.8255 (tttp) REVERT: A 550 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8370 (mt) REVERT: A 567 ARG cc_start: 0.7541 (tpt90) cc_final: 0.7197 (tpt-90) REVERT: A 635 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.7454 (mpp) REVERT: A 1045 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: A 1174 TRP cc_start: 0.7638 (t-100) cc_final: 0.7414 (t60) REVERT: A 1239 MET cc_start: 0.3070 (ptt) cc_final: 0.2458 (mtp) REVERT: A 1263 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7415 (ptm) REVERT: A 1340 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6133 (ttp80) REVERT: A 1714 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 8 ARG cc_start: 0.7203 (mtt180) cc_final: 0.6843 (mmp-170) REVERT: B 20 THR cc_start: 0.8020 (p) cc_final: 0.7793 (p) REVERT: B 32 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7914 (tmtt) REVERT: B 111 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7882 (ptm-80) REVERT: B 131 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7815 (ttmt) REVERT: B 272 LYS cc_start: 0.7847 (mtmt) cc_final: 0.7276 (mtmm) REVERT: B 276 SER cc_start: 0.7619 (OUTLIER) cc_final: 0.7315 (m) REVERT: B 280 ASN cc_start: 0.8239 (m-40) cc_final: 0.8026 (m-40) REVERT: B 321 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: B 325 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: B 327 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7699 (tp) REVERT: B 349 MET cc_start: 0.8048 (mtp) cc_final: 0.7687 (mtp) REVERT: B 422 MET cc_start: 0.4583 (mmm) cc_final: 0.4346 (mmm) REVERT: B 430 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8746 (m-80) REVERT: B 481 MET cc_start: 0.7926 (mtt) cc_final: 0.7551 (mtm) REVERT: B 542 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7220 (pt) REVERT: B 659 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: B 797 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7722 (mmpt) REVERT: B 844 LYS cc_start: 0.5934 (mmtt) cc_final: 0.5287 (mttp) REVERT: B 857 ASN cc_start: 0.8692 (p0) cc_final: 0.8460 (p0) REVERT: B 991 ASP cc_start: 0.7620 (p0) cc_final: 0.7005 (p0) REVERT: B 1005 MET cc_start: 0.9095 (mtt) cc_final: 0.8806 (mtt) REVERT: B 1114 TYR cc_start: 0.8533 (t80) cc_final: 0.8256 (t80) REVERT: C 134 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: C 135 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7086 (mm) REVERT: C 151 HIS cc_start: 0.6751 (OUTLIER) cc_final: 0.6466 (m90) REVERT: C 161 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7040 (pp20) REVERT: C 274 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7185 (ttt-90) REVERT: C 339 GLU cc_start: 0.7460 (tp30) cc_final: 0.7182 (tp30) REVERT: E 85 LYS cc_start: 0.7829 (mtpt) cc_final: 0.6975 (pmmt) REVERT: E 88 LYS cc_start: 0.7356 (mmmt) cc_final: 0.7092 (mtpp) REVERT: E 116 GLN cc_start: 0.7259 (tp40) cc_final: 0.6836 (tm130) REVERT: E 120 ASP cc_start: 0.7569 (m-30) cc_final: 0.6975 (m-30) REVERT: H 37 MET cc_start: 0.7807 (mtp) cc_final: 0.7595 (mtm) REVERT: H 80 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6807 (t70) REVERT: K 79 LYS cc_start: 0.8433 (ptpt) cc_final: 0.8145 (ptpp) REVERT: K 98 ARG cc_start: 0.8155 (ttp-170) cc_final: 0.7949 (ttp-170) REVERT: K 119 LYS cc_start: 0.8046 (tmtt) cc_final: 0.7783 (tmtm) REVERT: G 105 ILE cc_start: -0.0905 (mt) cc_final: -0.1171 (mt) outliers start: 204 outliers final: 67 residues processed: 843 average time/residue: 1.4134 time to fit residues: 1419.2381 Evaluate side-chains 587 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 494 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 TRP Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 206 PRO Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 1045 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1184 LYS Chi-restraints excluded: chain A residue 1186 GLU Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1340 ARG Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 429 PRO Chi-restraints excluded: chain B residue 430 PHE Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 797 LYS Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 866 CYS Chi-restraints excluded: chain B residue 1106 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 0.9990 chunk 304 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 chunk 162 optimal weight: 0.4980 chunk 315 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 234 optimal weight: 1.9990 chunk 365 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 ASN A 347 GLN A 395 GLN ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN A 486 ASN A 499 ASN A 551 ASN A 557 HIS A 564 HIS A 595 ASN A 600 GLN A 617 GLN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS A 728 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN A 847 GLN A 850 HIS A 859 ASN A 888 GLN A 918 GLN A1051 GLN A1067 HIS A1068 HIS A1076 GLN A1094 GLN A1097 GLN A1136 GLN A1177 GLN A1300 GLN A1329 GLN A1579 ASN A1717 GLN B 18 HIS B 97 ASN B 150 ASN B 219 HIS B 280 ASN B 313 ASN B 461 ASN B 473 HIS B 501 HIS B 523 GLN B 580 HIS ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN B 734 ASN B 846 ASN ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 GLN ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 945 HIS C 32 ASN C 59 ASN C 143 GLN C 166 HIS C 181 GLN C 290 ASN E 116 GLN E 133 GLN H 76 ASN I 8 ASN K 81 ASN K 85 GLN N 88 GLN M 34 GLN ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33855 Z= 0.214 Angle : 0.691 10.545 45947 Z= 0.362 Chirality : 0.047 0.213 5093 Planarity : 0.005 0.066 5797 Dihedral : 12.462 85.144 5116 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.00 % Favored : 92.90 % Rotamer: Outliers : 5.11 % Allowed : 14.87 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.53 (0.12), residues: 4001 helix: -0.89 (0.14), residues: 1205 sheet: -1.40 (0.20), residues: 637 loop : -2.28 (0.12), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 120 HIS 0.009 0.001 HIS A1509 PHE 0.018 0.002 PHE C 336 TYR 0.023 0.002 TYR B 828 ARG 0.005 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 544 time to evaluate : 4.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7470 (mtmt) cc_final: 0.7027 (mmtt) REVERT: A 127 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7556 (mt) REVERT: A 200 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8526 (mmp) REVERT: A 204 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6351 (mpp80) REVERT: A 381 GLN cc_start: 0.4505 (OUTLIER) cc_final: 0.3882 (tt0) REVERT: A 411 MET cc_start: 0.7224 (mpp) cc_final: 0.6862 (mpt) REVERT: A 535 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7497 (m) REVERT: A 550 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8220 (mm) REVERT: A 567 ARG cc_start: 0.7247 (tpt90) cc_final: 0.6876 (tpt-90) REVERT: A 635 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7254 (mtp) REVERT: A 973 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7107 (pt0) REVERT: A 1191 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7518 (ttp-110) REVERT: A 1239 MET cc_start: 0.3469 (ptt) cc_final: 0.2947 (mtp) REVERT: A 1340 ARG cc_start: 0.6312 (OUTLIER) cc_final: 0.5625 (ttp80) REVERT: A 1619 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7283 (mmt-90) REVERT: A 1637 ASP cc_start: 0.7897 (t70) cc_final: 0.7675 (t70) REVERT: A 1677 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7907 (m) REVERT: B 8 ARG cc_start: 0.7023 (mtt180) cc_final: 0.6649 (mmp-170) REVERT: B 20 THR cc_start: 0.7493 (p) cc_final: 0.7257 (p) REVERT: B 32 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7704 (tmtt) REVERT: B 111 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7826 (ptm160) REVERT: B 131 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7781 (ttmt) REVERT: B 272 LYS cc_start: 0.7682 (mtmt) cc_final: 0.7141 (mtmm) REVERT: B 325 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7115 (tp30) REVERT: B 430 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8807 (t80) REVERT: B 481 MET cc_start: 0.7780 (mtt) cc_final: 0.7483 (mtm) REVERT: B 659 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: B 797 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7534 (mmpt) REVERT: B 844 LYS cc_start: 0.5914 (mmtt) cc_final: 0.5468 (mmtp) REVERT: B 1018 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.6837 (mtp180) REVERT: B 1040 MET cc_start: 0.8660 (mtp) cc_final: 0.8441 (mtp) REVERT: B 1114 TYR cc_start: 0.8397 (t80) cc_final: 0.8121 (t80) REVERT: E 79 GLU cc_start: 0.7486 (mp0) cc_final: 0.7190 (mp0) REVERT: E 88 LYS cc_start: 0.7370 (mmmt) cc_final: 0.7133 (mmmt) REVERT: E 95 GLN cc_start: 0.7111 (pt0) cc_final: 0.6877 (pp30) REVERT: E 116 GLN cc_start: 0.7590 (tp-100) cc_final: 0.7132 (tm130) REVERT: E 128 GLU cc_start: 0.7367 (pt0) cc_final: 0.7116 (pt0) REVERT: E 143 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7052 (pt0) REVERT: H 37 MET cc_start: 0.7757 (mtp) cc_final: 0.7519 (mtm) REVERT: H 76 ASN cc_start: 0.8228 (m-40) cc_final: 0.8022 (m-40) REVERT: H 80 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6514 (t70) REVERT: K 79 LYS cc_start: 0.8476 (ptpt) cc_final: 0.8229 (pttp) REVERT: N 116 ARG cc_start: 0.4534 (OUTLIER) cc_final: 0.4200 (ttt90) REVERT: G 57 ILE cc_start: -0.0334 (mt) cc_final: -0.0678 (mp) REVERT: G 66 ARG cc_start: 0.0963 (mtm110) cc_final: 0.0723 (ptt90) REVERT: G 104 ASP cc_start: 0.0648 (p0) cc_final: 0.0257 (p0) REVERT: G 116 ILE cc_start: 0.1410 (OUTLIER) cc_final: 0.1126 (mm) REVERT: M 33 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6993 (pp) outliers start: 181 outliers final: 56 residues processed: 667 average time/residue: 1.4279 time to fit residues: 1139.3102 Evaluate side-chains 550 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 471 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 871 HIS Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1340 ARG Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 430 PHE Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 797 LYS Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain M residue 33 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 202 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 100 optimal weight: 0.2980 chunk 365 optimal weight: 9.9990 chunk 395 optimal weight: 6.9990 chunk 325 optimal weight: 2.9990 chunk 362 optimal weight: 0.0000 chunk 124 optimal weight: 0.9990 chunk 293 optimal weight: 3.9990 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS A 564 HIS A 632 GLN A 753 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN A1097 GLN ** A1109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 ASN B 147 ASN B 313 ASN B 365 ASN B 415 ASN B 468 HIS B 580 HIS B 625 ASN B 887 HIS B 889 GLN ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 972 ASN C 102 GLN C 143 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN H 44 ASN I 33 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33855 Z= 0.234 Angle : 0.650 10.202 45947 Z= 0.338 Chirality : 0.046 0.183 5093 Planarity : 0.005 0.064 5797 Dihedral : 11.622 83.225 5001 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.42 % Favored : 92.55 % Rotamer: Outliers : 5.25 % Allowed : 17.44 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.09 (0.13), residues: 4001 helix: -0.43 (0.15), residues: 1199 sheet: -1.35 (0.19), residues: 655 loop : -1.99 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 120 HIS 0.007 0.001 HIS A1509 PHE 0.018 0.001 PHE C 336 TYR 0.020 0.002 TYR A 579 ARG 0.006 0.000 ARG A1694 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 491 time to evaluate : 3.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7427 (mtmt) cc_final: 0.6989 (mmtt) REVERT: A 172 ASN cc_start: 0.7561 (t0) cc_final: 0.7182 (t0) REVERT: A 200 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8542 (mmp) REVERT: A 204 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6390 (mpp80) REVERT: A 381 GLN cc_start: 0.4389 (OUTLIER) cc_final: 0.4152 (tt0) REVERT: A 460 MET cc_start: 0.8263 (tpp) cc_final: 0.8058 (tpp) REVERT: A 478 GLN cc_start: 0.7425 (tt0) cc_final: 0.7081 (mp10) REVERT: A 550 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8288 (mm) REVERT: A 567 ARG cc_start: 0.7380 (tpt90) cc_final: 0.7004 (tpp80) REVERT: A 635 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7204 (mtp) REVERT: A 973 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7054 (pt0) REVERT: A 1122 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7499 (ttp80) REVERT: A 1191 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7579 (ttp-110) REVERT: A 1239 MET cc_start: 0.3432 (ptt) cc_final: 0.3062 (mtp) REVERT: A 1243 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8299 (mt) REVERT: A 1300 GLN cc_start: 0.5649 (OUTLIER) cc_final: 0.5377 (mm110) REVERT: A 1316 GLN cc_start: 0.5464 (OUTLIER) cc_final: 0.5000 (pp30) REVERT: A 1637 ASP cc_start: 0.7930 (t70) cc_final: 0.7686 (t0) REVERT: B 8 ARG cc_start: 0.7046 (mtt180) cc_final: 0.6817 (mmp-170) REVERT: B 20 THR cc_start: 0.7645 (p) cc_final: 0.7406 (p) REVERT: B 32 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7664 (tmtt) REVERT: B 111 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.8052 (ptt180) REVERT: B 131 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7794 (ttmt) REVERT: B 272 LYS cc_start: 0.7635 (mtmt) cc_final: 0.6964 (mtmm) REVERT: B 325 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7099 (tp30) REVERT: B 461 ASN cc_start: 0.7713 (t0) cc_final: 0.7423 (t0) REVERT: B 481 MET cc_start: 0.7784 (mtt) cc_final: 0.7470 (mtm) REVERT: B 548 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7427 (mtt180) REVERT: B 659 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7763 (tt0) REVERT: B 797 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7549 (mmtt) REVERT: B 844 LYS cc_start: 0.5756 (mmtt) cc_final: 0.5366 (mmtp) REVERT: B 902 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8628 (mmt) REVERT: B 1018 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.6689 (mtp180) REVERT: B 1040 MET cc_start: 0.8684 (mtp) cc_final: 0.8457 (mtp) REVERT: B 1114 TYR cc_start: 0.8396 (t80) cc_final: 0.8140 (t80) REVERT: C 298 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7317 (tmm160) REVERT: E 79 GLU cc_start: 0.7369 (mp0) cc_final: 0.7112 (mp0) REVERT: E 88 LYS cc_start: 0.7392 (mmmt) cc_final: 0.7094 (mmmt) REVERT: E 95 GLN cc_start: 0.7021 (pt0) cc_final: 0.6577 (pp30) REVERT: E 116 GLN cc_start: 0.7718 (tp-100) cc_final: 0.7217 (tm-30) REVERT: E 120 ASP cc_start: 0.7633 (m-30) cc_final: 0.7167 (m-30) REVERT: E 121 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6484 (mtt) REVERT: E 128 GLU cc_start: 0.7292 (pt0) cc_final: 0.7038 (pt0) REVERT: E 143 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7098 (pt0) REVERT: E 204 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8363 (mm) REVERT: H 37 MET cc_start: 0.7819 (mtp) cc_final: 0.7572 (mtm) REVERT: K 79 LYS cc_start: 0.8483 (ptpt) cc_final: 0.8229 (pttp) REVERT: N 116 ARG cc_start: 0.4500 (OUTLIER) cc_final: 0.4126 (ttt90) outliers start: 186 outliers final: 73 residues processed: 607 average time/residue: 1.4705 time to fit residues: 1072.5815 Evaluate side-chains 550 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 456 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1261 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1300 GLN Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 130 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 0.8980 chunk 274 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 367 optimal weight: 9.9990 chunk 388 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 347 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 557 HIS A 564 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN ** A1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN ** A1109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1118 GLN B 223 ASN B 329 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN B 580 HIS B 680 ASN ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 143 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 33855 Z= 0.339 Angle : 0.691 9.927 45947 Z= 0.357 Chirality : 0.048 0.254 5093 Planarity : 0.005 0.069 5797 Dihedral : 11.509 81.265 4981 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.87 % Favored : 92.10 % Rotamer: Outliers : 5.79 % Allowed : 18.85 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.00 (0.13), residues: 4001 helix: -0.41 (0.15), residues: 1208 sheet: -1.31 (0.19), residues: 656 loop : -1.90 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 120 HIS 0.008 0.001 HIS A 491 PHE 0.018 0.002 PHE C 336 TYR 0.023 0.002 TYR E 90 ARG 0.005 0.000 ARG A1694 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 475 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7415 (mtmt) cc_final: 0.6943 (mmtt) REVERT: A 127 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7687 (mt) REVERT: A 170 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6104 (mt0) REVERT: A 172 ASN cc_start: 0.7688 (t0) cc_final: 0.7371 (t0) REVERT: A 200 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8642 (mmp) REVERT: A 204 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6334 (mpp80) REVERT: A 478 GLN cc_start: 0.7559 (tt0) cc_final: 0.7123 (mp10) REVERT: A 550 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8310 (mm) REVERT: A 567 ARG cc_start: 0.7554 (tpt90) cc_final: 0.7175 (tpp80) REVERT: A 635 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.6958 (mtp) REVERT: A 973 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7160 (pt0) REVERT: A 1051 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6379 (pm20) REVERT: A 1191 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7699 (ttp-110) REVERT: A 1239 MET cc_start: 0.3352 (ptt) cc_final: 0.3034 (mtp) REVERT: A 1243 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8371 (mt) REVERT: A 1300 GLN cc_start: 0.5683 (OUTLIER) cc_final: 0.5427 (mm110) REVERT: A 1316 GLN cc_start: 0.5647 (OUTLIER) cc_final: 0.5204 (pp30) REVERT: A 1523 LEU cc_start: 0.4146 (OUTLIER) cc_final: 0.3683 (pp) REVERT: A 1637 ASP cc_start: 0.7948 (t70) cc_final: 0.7716 (t0) REVERT: B 8 ARG cc_start: 0.7020 (mtt180) cc_final: 0.6735 (mmp-170) REVERT: B 20 THR cc_start: 0.7626 (p) cc_final: 0.7385 (p) REVERT: B 32 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7614 (tmtt) REVERT: B 111 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8071 (ptt180) REVERT: B 131 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7834 (ttmt) REVERT: B 272 LYS cc_start: 0.7684 (mtmt) cc_final: 0.6951 (mtmm) REVERT: B 325 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7080 (tp30) REVERT: B 481 MET cc_start: 0.7824 (mtt) cc_final: 0.7505 (mtm) REVERT: B 550 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7749 (m-10) REVERT: B 659 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: B 797 LYS cc_start: 0.8075 (ttpt) cc_final: 0.7517 (mmpt) REVERT: B 1018 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.6525 (mtp180) REVERT: B 1040 MET cc_start: 0.8703 (mtp) cc_final: 0.8441 (mtp) REVERT: B 1068 HIS cc_start: 0.7228 (OUTLIER) cc_final: 0.6073 (p90) REVERT: B 1111 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8418 (m) REVERT: C 295 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.7769 (mmtt) REVERT: C 298 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7138 (tmm160) REVERT: E 79 GLU cc_start: 0.7382 (mp0) cc_final: 0.7136 (mt-10) REVERT: E 85 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7021 (pmmt) REVERT: E 88 LYS cc_start: 0.7319 (mmmt) cc_final: 0.6997 (mmmt) REVERT: E 95 GLN cc_start: 0.6906 (pt0) cc_final: 0.6588 (pp30) REVERT: E 116 GLN cc_start: 0.7796 (tp-100) cc_final: 0.7224 (tm-30) REVERT: E 121 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6412 (mtt) REVERT: E 128 GLU cc_start: 0.7383 (pt0) cc_final: 0.7126 (pt0) REVERT: E 143 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7131 (pt0) REVERT: E 174 GLN cc_start: 0.8364 (mm110) cc_final: 0.8115 (mm110) REVERT: H 37 MET cc_start: 0.7942 (mtp) cc_final: 0.7736 (mtm) REVERT: K 79 LYS cc_start: 0.8511 (ptpt) cc_final: 0.8251 (pttp) REVERT: K 119 LYS cc_start: 0.8058 (tmtt) cc_final: 0.7749 (tmtm) REVERT: N 116 ARG cc_start: 0.4694 (OUTLIER) cc_final: 0.4294 (ttt90) outliers start: 205 outliers final: 85 residues processed: 604 average time/residue: 1.4829 time to fit residues: 1066.1780 Evaluate side-chains 557 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 446 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1186 GLU Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1261 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1300 GLN Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1068 HIS Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1106 THR Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 116 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 323 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 289 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 331 optimal weight: 5.9990 chunk 268 optimal weight: 0.0020 chunk 0 optimal weight: 6.9990 chunk 198 optimal weight: 0.7980 chunk 348 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN ** A1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN ** A1109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 ASN B 223 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS B 889 GLN ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 972 ASN C 102 GLN C 143 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33855 Z= 0.251 Angle : 0.644 9.556 45947 Z= 0.332 Chirality : 0.045 0.230 5093 Planarity : 0.005 0.067 5797 Dihedral : 11.309 83.023 4976 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.67 % Favored : 92.30 % Rotamer: Outliers : 5.64 % Allowed : 20.24 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.83 (0.13), residues: 4001 helix: -0.22 (0.15), residues: 1215 sheet: -1.23 (0.19), residues: 651 loop : -1.82 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 120 HIS 0.005 0.001 HIS A 491 PHE 0.016 0.001 PHE I 19 TYR 0.026 0.002 TYR A 754 ARG 0.006 0.000 ARG A1122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 465 time to evaluate : 3.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7473 (mtmt) cc_final: 0.6999 (mmtt) REVERT: A 127 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7566 (mt) REVERT: A 139 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: A 172 ASN cc_start: 0.7701 (t0) cc_final: 0.7241 (t0) REVERT: A 200 MET cc_start: 0.8922 (tpt) cc_final: 0.8493 (mmp) REVERT: A 204 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6339 (mpp80) REVERT: A 478 GLN cc_start: 0.7551 (tt0) cc_final: 0.7144 (mp10) REVERT: A 550 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8376 (mm) REVERT: A 567 ARG cc_start: 0.7488 (tpt90) cc_final: 0.7127 (tpp80) REVERT: A 635 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.6895 (mtp) REVERT: A 973 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7104 (pt0) REVERT: A 1051 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6337 (pm20) REVERT: A 1119 GLU cc_start: 0.7464 (tp30) cc_final: 0.7223 (tp30) REVERT: A 1122 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7610 (ttp80) REVERT: A 1191 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7665 (ttp-110) REVERT: A 1239 MET cc_start: 0.3461 (ptt) cc_final: 0.3225 (mtp) REVERT: A 1243 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8355 (mt) REVERT: A 1300 GLN cc_start: 0.5695 (OUTLIER) cc_final: 0.5442 (mm110) REVERT: A 1316 GLN cc_start: 0.5636 (OUTLIER) cc_final: 0.5312 (pp30) REVERT: A 1637 ASP cc_start: 0.7892 (t70) cc_final: 0.7657 (t0) REVERT: B 8 ARG cc_start: 0.7095 (mtt180) cc_final: 0.6823 (mmp-170) REVERT: B 20 THR cc_start: 0.7588 (p) cc_final: 0.7359 (p) REVERT: B 32 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7352 (tmtt) REVERT: B 131 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7818 (ttmt) REVERT: B 272 LYS cc_start: 0.7635 (mtmt) cc_final: 0.6865 (mtmm) REVERT: B 325 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6966 (tp30) REVERT: B 481 MET cc_start: 0.7796 (mtt) cc_final: 0.7528 (mtm) REVERT: B 550 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.7365 (m-10) REVERT: B 659 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: B 797 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7513 (mmtt) REVERT: B 844 LYS cc_start: 0.6123 (mmpt) cc_final: 0.5612 (mmtp) REVERT: B 1018 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.6462 (mtp180) REVERT: B 1040 MET cc_start: 0.8675 (mtp) cc_final: 0.8430 (mtp) REVERT: B 1068 HIS cc_start: 0.7249 (OUTLIER) cc_final: 0.6106 (p90) REVERT: B 1108 ASP cc_start: 0.6586 (t0) cc_final: 0.6051 (t0) REVERT: B 1111 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8417 (m) REVERT: C 295 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7759 (mmtt) REVERT: C 298 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7078 (tmm160) REVERT: E 79 GLU cc_start: 0.7365 (mp0) cc_final: 0.7135 (mt-10) REVERT: E 85 LYS cc_start: 0.7835 (mtpt) cc_final: 0.7026 (pmmt) REVERT: E 88 LYS cc_start: 0.7383 (mmmt) cc_final: 0.7013 (mmmt) REVERT: E 121 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6409 (mtt) REVERT: E 128 GLU cc_start: 0.7387 (pt0) cc_final: 0.7156 (pt0) REVERT: E 143 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7109 (pt0) REVERT: H 37 MET cc_start: 0.7959 (mtp) cc_final: 0.7736 (mtm) REVERT: H 140 ARG cc_start: 0.8266 (mpt90) cc_final: 0.8050 (mmt-90) REVERT: I 29 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5683 (tp) REVERT: J 58 LYS cc_start: 0.8638 (mttp) cc_final: 0.8433 (mtmt) REVERT: K 60 MET cc_start: 0.7877 (mmp) cc_final: 0.7582 (mtp) REVERT: K 79 LYS cc_start: 0.8564 (ptpt) cc_final: 0.8277 (pttp) REVERT: K 119 LYS cc_start: 0.8066 (tmtt) cc_final: 0.7755 (tmtm) REVERT: N 63 LEU cc_start: 0.2749 (OUTLIER) cc_final: 0.2480 (mm) REVERT: N 116 ARG cc_start: 0.4732 (OUTLIER) cc_final: 0.4405 (ttt90) REVERT: M 39 MET cc_start: 0.4865 (ppp) cc_final: 0.4394 (pmm) outliers start: 200 outliers final: 86 residues processed: 600 average time/residue: 1.4765 time to fit residues: 1055.9377 Evaluate side-chains 551 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 440 time to evaluate : 3.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 878 LYS Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1186 GLU Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1261 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1300 GLN Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1068 HIS Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain M residue 103 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 130 optimal weight: 2.9990 chunk 349 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 228 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 388 optimal weight: 4.9990 chunk 322 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 204 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN A1109 ASN B 223 ASN B 320 ASN B 371 ASN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS B 889 GLN ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN E 116 GLN H 44 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33855 Z= 0.243 Angle : 0.631 9.741 45947 Z= 0.326 Chirality : 0.045 0.194 5093 Planarity : 0.005 0.066 5797 Dihedral : 11.130 83.758 4968 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.87 % Favored : 92.10 % Rotamer: Outliers : 5.36 % Allowed : 21.56 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.64 (0.13), residues: 4001 helix: -0.04 (0.15), residues: 1202 sheet: -1.08 (0.20), residues: 641 loop : -1.73 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 120 HIS 0.006 0.001 HIS A 557 PHE 0.017 0.001 PHE C 336 TYR 0.019 0.002 TYR A 754 ARG 0.006 0.000 ARG A1694 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 457 time to evaluate : 3.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7499 (mtmt) cc_final: 0.7003 (mmtt) REVERT: A 127 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7560 (mt) REVERT: A 139 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7368 (tt0) REVERT: A 172 ASN cc_start: 0.7864 (t0) cc_final: 0.7594 (t0) REVERT: A 200 MET cc_start: 0.8884 (tpt) cc_final: 0.8329 (mmp) REVERT: A 204 ARG cc_start: 0.6788 (mpp-170) cc_final: 0.6335 (mpp80) REVERT: A 478 GLN cc_start: 0.7548 (tt0) cc_final: 0.7175 (mp10) REVERT: A 521 GLN cc_start: 0.7047 (mp10) cc_final: 0.6583 (mm-40) REVERT: A 550 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8119 (mt) REVERT: A 567 ARG cc_start: 0.7510 (tpt90) cc_final: 0.7145 (tpp80) REVERT: A 635 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.6830 (mpp) REVERT: A 973 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7119 (pt0) REVERT: A 1051 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.6265 (pm20) REVERT: A 1191 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7651 (ttp-110) REVERT: A 1239 MET cc_start: 0.3539 (ptt) cc_final: 0.3097 (mtp) REVERT: A 1243 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8333 (mt) REVERT: A 1316 GLN cc_start: 0.5844 (OUTLIER) cc_final: 0.5492 (pp30) REVERT: B 20 THR cc_start: 0.7594 (p) cc_final: 0.7344 (p) REVERT: B 272 LYS cc_start: 0.7471 (mtmt) cc_final: 0.6734 (mtmm) REVERT: B 325 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6968 (tp30) REVERT: B 481 MET cc_start: 0.7782 (mtt) cc_final: 0.7477 (mtm) REVERT: B 550 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.7379 (m-10) REVERT: B 659 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: B 797 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7481 (mmpt) REVERT: B 835 GLU cc_start: 0.6890 (pt0) cc_final: 0.6626 (pt0) REVERT: B 844 LYS cc_start: 0.6085 (mmpt) cc_final: 0.5561 (mmtp) REVERT: B 1018 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.6433 (mtp180) REVERT: B 1040 MET cc_start: 0.8678 (mtp) cc_final: 0.8439 (mtp) REVERT: B 1068 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6092 (p90) REVERT: B 1108 ASP cc_start: 0.6569 (t0) cc_final: 0.6283 (t70) REVERT: C 295 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7790 (mmtt) REVERT: C 298 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7064 (tmm160) REVERT: E 79 GLU cc_start: 0.7351 (mp0) cc_final: 0.7149 (mt-10) REVERT: E 85 LYS cc_start: 0.7842 (mtpt) cc_final: 0.6984 (pmmt) REVERT: E 88 LYS cc_start: 0.7409 (mmmt) cc_final: 0.7068 (mmmt) REVERT: E 143 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7123 (pt0) REVERT: E 174 GLN cc_start: 0.8319 (mm110) cc_final: 0.8044 (mm110) REVERT: E 204 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8421 (mm) REVERT: H 37 MET cc_start: 0.7969 (mtp) cc_final: 0.7692 (mtm) REVERT: H 38 ASP cc_start: 0.7543 (m-30) cc_final: 0.7188 (m-30) REVERT: H 140 ARG cc_start: 0.8259 (mpt90) cc_final: 0.8041 (mmt-90) REVERT: I 29 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5614 (tp) REVERT: J 58 LYS cc_start: 0.8634 (mttp) cc_final: 0.8414 (mtmt) REVERT: K 79 LYS cc_start: 0.8555 (ptpt) cc_final: 0.8219 (pttp) REVERT: K 119 LYS cc_start: 0.8061 (tmtt) cc_final: 0.7768 (tmtm) REVERT: N 63 LEU cc_start: 0.2748 (OUTLIER) cc_final: 0.2513 (mm) REVERT: N 116 ARG cc_start: 0.4794 (OUTLIER) cc_final: 0.4453 (ttt90) REVERT: G 181 VAL cc_start: -0.0887 (OUTLIER) cc_final: -0.1125 (m) REVERT: M 39 MET cc_start: 0.5100 (OUTLIER) cc_final: 0.4761 (mpm) outliers start: 190 outliers final: 86 residues processed: 583 average time/residue: 1.4963 time to fit residues: 1042.8656 Evaluate side-chains 556 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 447 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1186 GLU Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1261 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1692 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1068 HIS Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain M residue 103 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 374 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 327 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 387 optimal weight: 20.0000 chunk 242 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN ** A1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 329 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS B 941 HIS C 143 GLN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN H 76 ASN M 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 33855 Z= 0.385 Angle : 0.719 12.198 45947 Z= 0.368 Chirality : 0.049 0.213 5093 Planarity : 0.005 0.068 5797 Dihedral : 11.209 83.036 4957 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.35 % Favored : 91.63 % Rotamer: Outliers : 5.76 % Allowed : 21.17 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.85 (0.13), residues: 4001 helix: -0.31 (0.15), residues: 1216 sheet: -1.21 (0.19), residues: 676 loop : -1.80 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 120 HIS 0.006 0.001 HIS A 80 PHE 0.016 0.002 PHE A 795 TYR 0.022 0.002 TYR E 90 ARG 0.006 0.000 ARG B 978 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 450 time to evaluate : 3.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7507 (mtmt) cc_final: 0.6993 (mmtt) REVERT: A 127 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7704 (mt) REVERT: A 170 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6105 (mp10) REVERT: A 200 MET cc_start: 0.8881 (tpt) cc_final: 0.8387 (mmp) REVERT: A 204 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6359 (mpp80) REVERT: A 345 MET cc_start: 0.4861 (OUTLIER) cc_final: 0.3685 (mtt) REVERT: A 478 GLN cc_start: 0.7601 (tt0) cc_final: 0.7104 (mp10) REVERT: A 550 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8151 (mt) REVERT: A 567 ARG cc_start: 0.7668 (tpt90) cc_final: 0.7306 (tpp80) REVERT: A 635 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.6813 (mpp) REVERT: A 754 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6201 (m-10) REVERT: A 973 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7178 (pt0) REVERT: A 1051 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.6316 (pm20) REVERT: A 1122 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7584 (ttp80) REVERT: A 1191 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7750 (ttp-110) REVERT: A 1239 MET cc_start: 0.3483 (ptt) cc_final: 0.2930 (OUTLIER) REVERT: A 1243 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8389 (mt) REVERT: A 1283 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6535 (mttt) REVERT: A 1300 GLN cc_start: 0.5801 (OUTLIER) cc_final: 0.5551 (mm110) REVERT: A 1316 GLN cc_start: 0.5862 (OUTLIER) cc_final: 0.5495 (pp30) REVERT: B 20 THR cc_start: 0.7660 (p) cc_final: 0.7403 (p) REVERT: B 272 LYS cc_start: 0.7545 (mtmt) cc_final: 0.6933 (mttp) REVERT: B 325 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7003 (tp30) REVERT: B 481 MET cc_start: 0.7798 (mtt) cc_final: 0.7476 (mtm) REVERT: B 550 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7624 (m-10) REVERT: B 659 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: B 1018 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8257 (mtp180) REVERT: B 1040 MET cc_start: 0.8689 (mtp) cc_final: 0.8412 (mtp) REVERT: B 1068 HIS cc_start: 0.7267 (OUTLIER) cc_final: 0.6107 (p90) REVERT: B 1108 ASP cc_start: 0.6601 (t0) cc_final: 0.6322 (t70) REVERT: B 1111 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8481 (m) REVERT: C 295 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.7859 (mmtt) REVERT: C 298 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7074 (tmm160) REVERT: E 79 GLU cc_start: 0.7414 (mp0) cc_final: 0.7168 (mt-10) REVERT: E 85 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7027 (pmmt) REVERT: E 88 LYS cc_start: 0.7328 (mmmt) cc_final: 0.6955 (mmmt) REVERT: E 143 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7163 (pt0) REVERT: E 174 GLN cc_start: 0.8294 (mm110) cc_final: 0.8013 (mm110) REVERT: H 37 MET cc_start: 0.8096 (mtp) cc_final: 0.7859 (mtm) REVERT: I 29 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5751 (tp) REVERT: J 58 LYS cc_start: 0.8663 (mttp) cc_final: 0.8435 (mtmt) REVERT: K 79 LYS cc_start: 0.8555 (ptpt) cc_final: 0.8226 (pttp) REVERT: K 119 LYS cc_start: 0.8088 (tmtt) cc_final: 0.7809 (tmtm) REVERT: N 16 PRO cc_start: 0.5332 (Cg_endo) cc_final: 0.4803 (Cg_exo) REVERT: N 44 LEU cc_start: 0.5278 (mt) cc_final: 0.4643 (tt) REVERT: N 63 LEU cc_start: 0.2596 (OUTLIER) cc_final: 0.2353 (mm) REVERT: N 116 ARG cc_start: 0.4984 (OUTLIER) cc_final: 0.4546 (ttt90) REVERT: M 39 MET cc_start: 0.5364 (OUTLIER) cc_final: 0.4982 (mmp) REVERT: M 109 MET cc_start: 0.7097 (tpt) cc_final: 0.6619 (tpp) outliers start: 204 outliers final: 102 residues processed: 581 average time/residue: 1.4806 time to fit residues: 1025.5902 Evaluate side-chains 566 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 438 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1011 ASP Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1186 GLU Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1261 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1283 LYS Chi-restraints excluded: chain A residue 1300 GLN Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1651 GLU Chi-restraints excluded: chain A residue 1692 GLU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1068 HIS Chi-restraints excluded: chain B residue 1106 THR Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain M residue 103 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 239 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 116 optimal weight: 0.0270 chunk 76 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 246 optimal weight: 0.6980 chunk 263 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 304 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN ** A1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS B 889 GLN C 143 GLN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN H 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33855 Z= 0.197 Angle : 0.628 11.522 45947 Z= 0.321 Chirality : 0.044 0.172 5093 Planarity : 0.005 0.065 5797 Dihedral : 10.966 85.726 4953 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.35 % Favored : 92.60 % Rotamer: Outliers : 4.26 % Allowed : 22.78 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.55 (0.13), residues: 4001 helix: 0.06 (0.15), residues: 1205 sheet: -1.01 (0.20), residues: 642 loop : -1.70 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 120 HIS 0.003 0.001 HIS B 918 PHE 0.016 0.001 PHE C 336 TYR 0.016 0.001 TYR E 90 ARG 0.006 0.000 ARG A1694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 470 time to evaluate : 3.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7553 (mtmt) cc_final: 0.6935 (mmtt) REVERT: A 127 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7550 (mt) REVERT: A 170 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.5872 (mp10) REVERT: A 200 MET cc_start: 0.8833 (tpt) cc_final: 0.8530 (mmp) REVERT: A 204 ARG cc_start: 0.6790 (mpp-170) cc_final: 0.6345 (mpp80) REVERT: A 478 GLN cc_start: 0.7511 (tt0) cc_final: 0.7140 (mp10) REVERT: A 521 GLN cc_start: 0.7016 (mp10) cc_final: 0.6524 (mm-40) REVERT: A 567 ARG cc_start: 0.7487 (tpt90) cc_final: 0.7126 (tpp80) REVERT: A 874 ASN cc_start: 0.7424 (m-40) cc_final: 0.7179 (m-40) REVERT: A 973 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7104 (pt0) REVERT: A 1056 VAL cc_start: 0.7914 (t) cc_final: 0.7657 (p) REVERT: A 1191 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7660 (ttp-110) REVERT: A 1239 MET cc_start: 0.3452 (ptt) cc_final: 0.2975 (mtp) REVERT: A 1243 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8336 (mt) REVERT: A 1316 GLN cc_start: 0.5816 (OUTLIER) cc_final: 0.5496 (pp30) REVERT: A 1498 MET cc_start: 0.6007 (mmp) cc_final: 0.5704 (mmm) REVERT: B 20 THR cc_start: 0.7567 (p) cc_final: 0.7325 (p) REVERT: B 272 LYS cc_start: 0.7445 (mtmt) cc_final: 0.6736 (mtmt) REVERT: B 325 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6981 (tp30) REVERT: B 481 MET cc_start: 0.7750 (mtt) cc_final: 0.7450 (mtm) REVERT: B 550 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.7292 (m-10) REVERT: B 659 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: B 797 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7476 (mmtt) REVERT: B 844 LYS cc_start: 0.6254 (mmpt) cc_final: 0.5713 (mmtp) REVERT: B 1018 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.6865 (mtp180) REVERT: B 1068 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6172 (p90) REVERT: B 1108 ASP cc_start: 0.6632 (t0) cc_final: 0.6358 (t70) REVERT: B 1111 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8429 (m) REVERT: C 243 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6681 (pm20) REVERT: C 295 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.7798 (mmtt) REVERT: E 88 LYS cc_start: 0.7389 (mmmt) cc_final: 0.7018 (mmmt) REVERT: E 143 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7125 (pt0) REVERT: E 174 GLN cc_start: 0.8209 (mm110) cc_final: 0.7944 (mm110) REVERT: H 15 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8036 (mm) REVERT: H 37 MET cc_start: 0.7964 (mtp) cc_final: 0.7644 (mtm) REVERT: H 38 ASP cc_start: 0.7495 (m-30) cc_final: 0.7144 (m-30) REVERT: I 29 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5869 (tp) REVERT: J 58 LYS cc_start: 0.8659 (mttp) cc_final: 0.8362 (mtmt) REVERT: K 79 LYS cc_start: 0.8550 (ptpt) cc_final: 0.8029 (pttp) REVERT: K 119 LYS cc_start: 0.8021 (tmtt) cc_final: 0.7750 (tmtm) REVERT: N 16 PRO cc_start: 0.5375 (Cg_endo) cc_final: 0.4810 (Cg_exo) REVERT: N 44 LEU cc_start: 0.5224 (mt) cc_final: 0.4639 (tt) REVERT: N 63 LEU cc_start: 0.2526 (OUTLIER) cc_final: 0.2325 (mm) REVERT: N 116 ARG cc_start: 0.4957 (OUTLIER) cc_final: 0.4655 (ttt90) REVERT: M 39 MET cc_start: 0.5268 (OUTLIER) cc_final: 0.4884 (mmp) REVERT: M 109 MET cc_start: 0.7063 (tpt) cc_final: 0.6633 (tpp) outliers start: 151 outliers final: 78 residues processed: 570 average time/residue: 1.4683 time to fit residues: 997.9462 Evaluate side-chains 541 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 444 time to evaluate : 3.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1651 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1068 HIS Chi-restraints excluded: chain B residue 1106 THR Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain M residue 39 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 0.9980 chunk 371 optimal weight: 1.9990 chunk 338 optimal weight: 4.9990 chunk 361 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 283 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 326 optimal weight: 3.9990 chunk 341 optimal weight: 0.6980 chunk 359 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN ** A1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1118 GLN B 223 ASN B 580 HIS B 889 GLN C 143 GLN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33855 Z= 0.273 Angle : 0.656 12.109 45947 Z= 0.336 Chirality : 0.046 0.176 5093 Planarity : 0.005 0.067 5797 Dihedral : 10.864 84.977 4944 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.02 % Favored : 91.95 % Rotamer: Outliers : 3.84 % Allowed : 23.37 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.58 (0.13), residues: 4001 helix: -0.02 (0.15), residues: 1217 sheet: -1.04 (0.20), residues: 626 loop : -1.67 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 120 HIS 0.007 0.001 HIS A 557 PHE 0.016 0.001 PHE C 336 TYR 0.025 0.002 TYR A 754 ARG 0.007 0.000 ARG A1694 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 448 time to evaluate : 3.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7589 (mtmt) cc_final: 0.7039 (mmtt) REVERT: A 127 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7614 (mt) REVERT: A 170 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.5826 (mp10) REVERT: A 200 MET cc_start: 0.8876 (tpt) cc_final: 0.8587 (mmp) REVERT: A 204 ARG cc_start: 0.6757 (mpp-170) cc_final: 0.6313 (mpp80) REVERT: A 478 GLN cc_start: 0.7534 (tt0) cc_final: 0.7090 (mp10) REVERT: A 521 GLN cc_start: 0.7148 (mp10) cc_final: 0.6639 (mm-40) REVERT: A 550 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8192 (mt) REVERT: A 567 ARG cc_start: 0.7554 (tpt90) cc_final: 0.7186 (tpp80) REVERT: A 635 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.6752 (mpp) REVERT: A 973 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7140 (pt0) REVERT: A 1051 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6379 (pm20) REVERT: A 1191 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7692 (ttp-110) REVERT: A 1239 MET cc_start: 0.3421 (ptt) cc_final: 0.2930 (mtp) REVERT: A 1316 GLN cc_start: 0.5825 (OUTLIER) cc_final: 0.5515 (pp30) REVERT: A 1540 MET cc_start: 0.3532 (OUTLIER) cc_final: 0.3302 (mtt) REVERT: B 20 THR cc_start: 0.7654 (p) cc_final: 0.7411 (p) REVERT: B 272 LYS cc_start: 0.7507 (mtmt) cc_final: 0.6819 (mtmt) REVERT: B 325 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6973 (tp30) REVERT: B 481 MET cc_start: 0.7759 (mtt) cc_final: 0.7450 (mtm) REVERT: B 550 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7526 (m-10) REVERT: B 659 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: B 844 LYS cc_start: 0.6275 (mmpt) cc_final: 0.5651 (mmtp) REVERT: B 1018 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8217 (mtp180) REVERT: B 1068 HIS cc_start: 0.7224 (OUTLIER) cc_final: 0.6392 (p90) REVERT: B 1095 LYS cc_start: 0.7569 (ptpp) cc_final: 0.7274 (ptmt) REVERT: B 1108 ASP cc_start: 0.6686 (t0) cc_final: 0.6428 (t70) REVERT: B 1111 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8439 (m) REVERT: C 243 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6686 (pm20) REVERT: C 295 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.7856 (mmtt) REVERT: E 88 LYS cc_start: 0.7436 (mmmt) cc_final: 0.7076 (mmmt) REVERT: E 143 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7138 (pt0) REVERT: E 174 GLN cc_start: 0.8197 (mm110) cc_final: 0.7941 (mm110) REVERT: H 37 MET cc_start: 0.8001 (mtp) cc_final: 0.7679 (mtm) REVERT: H 38 ASP cc_start: 0.7487 (m-30) cc_final: 0.7168 (m-30) REVERT: H 140 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8077 (mmt-90) REVERT: I 29 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5923 (tp) REVERT: J 58 LYS cc_start: 0.8643 (mttp) cc_final: 0.8359 (mtmt) REVERT: K 79 LYS cc_start: 0.8544 (ptpt) cc_final: 0.8020 (pttp) REVERT: K 119 LYS cc_start: 0.8046 (tmtt) cc_final: 0.7778 (tmtm) REVERT: N 16 PRO cc_start: 0.5567 (Cg_endo) cc_final: 0.4950 (Cg_exo) REVERT: N 44 LEU cc_start: 0.5286 (mt) cc_final: 0.4682 (tt) REVERT: N 116 ARG cc_start: 0.5105 (OUTLIER) cc_final: 0.4677 (ttt90) REVERT: M 39 MET cc_start: 0.5524 (OUTLIER) cc_final: 0.5053 (mmp) REVERT: M 109 MET cc_start: 0.7083 (tpt) cc_final: 0.6581 (tpp) outliers start: 136 outliers final: 81 residues processed: 540 average time/residue: 1.4873 time to fit residues: 957.3983 Evaluate side-chains 542 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 440 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1540 MET Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1651 GLU Chi-restraints excluded: chain A residue 1692 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1018 ARG Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1068 HIS Chi-restraints excluded: chain B residue 1106 THR Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain M residue 39 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 237 optimal weight: 2.9990 chunk 381 optimal weight: 30.0000 chunk 233 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 chunk 400 optimal weight: 4.9990 chunk 368 optimal weight: 3.9990 chunk 318 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 246 optimal weight: 0.6980 chunk 195 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 580 HIS B 889 GLN C 143 GLN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN H 44 ASN H 130 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33855 Z= 0.230 Angle : 0.636 9.863 45947 Z= 0.327 Chirality : 0.045 0.163 5093 Planarity : 0.005 0.065 5797 Dihedral : 10.805 85.927 4942 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.55 % Favored : 92.43 % Rotamer: Outliers : 3.39 % Allowed : 23.77 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 4001 helix: 0.11 (0.15), residues: 1209 sheet: -0.99 (0.20), residues: 626 loop : -1.63 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 120 HIS 0.006 0.001 HIS A 557 PHE 0.016 0.001 PHE C 336 TYR 0.017 0.001 TYR A1591 ARG 0.007 0.000 ARG A1694 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 444 time to evaluate : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7532 (mtmt) cc_final: 0.6992 (mmtt) REVERT: A 127 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7584 (mt) REVERT: A 170 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.5759 (mp10) REVERT: A 200 MET cc_start: 0.8845 (tpt) cc_final: 0.8537 (mmp) REVERT: A 204 ARG cc_start: 0.6797 (mpp-170) cc_final: 0.6310 (mpp80) REVERT: A 478 GLN cc_start: 0.7516 (tt0) cc_final: 0.7089 (mp10) REVERT: A 521 GLN cc_start: 0.7162 (mp10) cc_final: 0.6714 (mm-40) REVERT: A 550 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8149 (mt) REVERT: A 567 ARG cc_start: 0.7494 (tpt90) cc_final: 0.7143 (tpp80) REVERT: A 635 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.6746 (mpp) REVERT: A 874 ASN cc_start: 0.7432 (m-40) cc_final: 0.7171 (m-40) REVERT: A 973 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7155 (pt0) REVERT: A 1051 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.6382 (pm20) REVERT: A 1191 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7669 (ttp-110) REVERT: A 1239 MET cc_start: 0.3450 (ptt) cc_final: 0.2932 (mtp) REVERT: A 1316 GLN cc_start: 0.5807 (OUTLIER) cc_final: 0.5512 (pp30) REVERT: A 1342 MET cc_start: 0.4571 (OUTLIER) cc_final: 0.4042 (mmp) REVERT: A 1523 LEU cc_start: 0.3690 (OUTLIER) cc_final: 0.3313 (pp) REVERT: A 1540 MET cc_start: 0.3301 (OUTLIER) cc_final: 0.3083 (mtt) REVERT: B 20 THR cc_start: 0.7584 (p) cc_final: 0.7336 (p) REVERT: B 272 LYS cc_start: 0.7488 (mtmt) cc_final: 0.6805 (mtmt) REVERT: B 325 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: B 428 LYS cc_start: 0.8296 (mttp) cc_final: 0.7820 (mtmt) REVERT: B 481 MET cc_start: 0.7741 (mtt) cc_final: 0.7443 (mtm) REVERT: B 550 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.7397 (m-10) REVERT: B 659 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: B 797 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7470 (mmtt) REVERT: B 842 LYS cc_start: 0.7555 (ptpt) cc_final: 0.7347 (mmtm) REVERT: B 844 LYS cc_start: 0.6219 (mmpt) cc_final: 0.5662 (mmtp) REVERT: B 1068 HIS cc_start: 0.7210 (OUTLIER) cc_final: 0.6433 (p90) REVERT: B 1095 LYS cc_start: 0.7599 (ptpp) cc_final: 0.7324 (ptmt) REVERT: B 1108 ASP cc_start: 0.6694 (t0) cc_final: 0.6436 (t70) REVERT: B 1111 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8498 (m) REVERT: C 295 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7844 (mmtt) REVERT: E 88 LYS cc_start: 0.7369 (mmmt) cc_final: 0.6984 (mmmt) REVERT: E 143 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7128 (pt0) REVERT: E 174 GLN cc_start: 0.8206 (mm110) cc_final: 0.7947 (mm110) REVERT: H 37 MET cc_start: 0.7981 (mtp) cc_final: 0.7656 (mtm) REVERT: H 38 ASP cc_start: 0.7505 (m-30) cc_final: 0.7190 (m-30) REVERT: H 140 ARG cc_start: 0.8302 (mpt90) cc_final: 0.8071 (mmt-90) REVERT: J 58 LYS cc_start: 0.8664 (mttp) cc_final: 0.8361 (mtmt) REVERT: K 79 LYS cc_start: 0.8544 (ptpt) cc_final: 0.8025 (pttp) REVERT: K 119 LYS cc_start: 0.8006 (tmtt) cc_final: 0.7747 (tmtm) REVERT: N 16 PRO cc_start: 0.5626 (Cg_endo) cc_final: 0.5032 (Cg_exo) REVERT: N 44 LEU cc_start: 0.5267 (mt) cc_final: 0.4678 (tt) REVERT: N 116 ARG cc_start: 0.5046 (OUTLIER) cc_final: 0.4669 (ttt90) REVERT: M 39 MET cc_start: 0.5449 (OUTLIER) cc_final: 0.5008 (mmp) REVERT: M 109 MET cc_start: 0.7145 (tpt) cc_final: 0.6663 (tpp) outliers start: 120 outliers final: 86 residues processed: 527 average time/residue: 1.4967 time to fit residues: 945.2301 Evaluate side-chains 541 residues out of total 3544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 435 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1342 MET Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1540 MET Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1651 GLU Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1068 HIS Chi-restraints excluded: chain B residue 1106 THR Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain M residue 39 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 253 optimal weight: 7.9990 chunk 339 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 294 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 319 optimal weight: 0.6980 chunk 133 optimal weight: 0.0670 chunk 327 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN B 223 ASN B 580 HIS B 889 GLN B1011 GLN C 143 GLN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN H 130 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.175689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.137243 restraints weight = 36483.995| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.71 r_work: 0.3406 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33855 Z= 0.195 Angle : 0.614 12.346 45947 Z= 0.314 Chirality : 0.044 0.160 5093 Planarity : 0.005 0.064 5797 Dihedral : 10.660 86.755 4942 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.45 % Favored : 92.50 % Rotamer: Outliers : 3.27 % Allowed : 24.27 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.33 (0.13), residues: 4001 helix: 0.26 (0.15), residues: 1216 sheet: -0.90 (0.20), residues: 630 loop : -1.57 (0.13), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP B 120 HIS 0.005 0.001 HIS A 557 PHE 0.015 0.001 PHE I 19 TYR 0.029 0.001 TYR B 303 ARG 0.008 0.000 ARG A 504 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15015.74 seconds wall clock time: 265 minutes 50.38 seconds (15950.38 seconds total)