Starting phenix.real_space_refine on Sat Mar 23 11:21:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn3_30779/03_2024/7dn3_30779_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn3_30779/03_2024/7dn3_30779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn3_30779/03_2024/7dn3_30779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn3_30779/03_2024/7dn3_30779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn3_30779/03_2024/7dn3_30779_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn3_30779/03_2024/7dn3_30779_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.049 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 P 45 5.49 5 Mg 1 5.21 5 S 249 5.16 5 C 23212 2.51 5 N 6411 2.21 5 O 6928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A ASP 544": "OD1" <-> "OD2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A ARG 816": "NH1" <-> "NH2" Residue "A GLU 822": "OE1" <-> "OE2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A GLU 880": "OE1" <-> "OE2" Residue "A GLU 996": "OE1" <-> "OE2" Residue "A ARG 998": "NH1" <-> "NH2" Residue "A ARG 1069": "NH1" <-> "NH2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A ARG 1141": "NH1" <-> "NH2" Residue "A GLU 1143": "OE1" <-> "OE2" Residue "A GLU 1170": "OE1" <-> "OE2" Residue "A ARG 1178": "NH1" <-> "NH2" Residue "A GLU 1179": "OE1" <-> "OE2" Residue "A GLU 1206": "OE1" <-> "OE2" Residue "A ARG 1245": "NH1" <-> "NH2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 529": "OE1" <-> "OE2" Residue "B GLU 530": "OE1" <-> "OE2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 726": "OE1" <-> "OE2" Residue "B ARG 764": "NH1" <-> "NH2" Residue "B ARG 781": "NH1" <-> "NH2" Residue "B ARG 1041": "NH1" <-> "NH2" Residue "B ARG 1052": "NH1" <-> "NH2" Residue "B GLU 1066": "OE1" <-> "OE2" Residue "C GLU 9": "OE1" <-> "OE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C ARG 298": "NH1" <-> "NH2" Residue "G ARG 12": "NH1" <-> "NH2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 16": "OE1" <-> "OE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 48": "OD1" <-> "OD2" Residue "K GLU 115": "OE1" <-> "OE2" Residue "L GLU 21": "OE1" <-> "OE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "P GLU 233": "OE1" <-> "OE2" Residue "P GLU 257": "OE1" <-> "OE2" Residue "P ASP 294": "OD1" <-> "OD2" Residue "P GLU 301": "OE1" <-> "OE2" Residue "P GLU 312": "OE1" <-> "OE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 5": "OE1" <-> "OE2" Residue "O TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 134": "OE1" <-> "OE2" Residue "O ARG 159": "NH1" <-> "NH2" Residue "O ARG 258": "NH1" <-> "NH2" Residue "O GLU 408": "OE1" <-> "OE2" Residue "O ARG 419": "NH1" <-> "NH2" Residue "O PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 448": "OE1" <-> "OE2" Residue "O GLU 453": "OE1" <-> "OE2" Residue "O GLU 456": "OE1" <-> "OE2" Residue "O GLU 500": "OE1" <-> "OE2" Residue "O GLU 513": "OE1" <-> "OE2" Residue "O ARG 533": "NH1" <-> "NH2" Residue "Q TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 52": "OE1" <-> "OE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q ASP 83": "OD1" <-> "OD2" Residue "Q GLU 85": "OE1" <-> "OE2" Residue "Q ARG 105": "NH1" <-> "NH2" Residue "Q ARG 108": "NH1" <-> "NH2" Residue "D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "M TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M ARG 113": "NH1" <-> "NH2" Residue "M ARG 136": "NH1" <-> "NH2" Residue "M ASP 146": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36856 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 10152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1293, 10152 Classifications: {'peptide': 1293} Link IDs: {'PTRANS': 60, 'TRANS': 1232} Chain breaks: 5 Chain: "B" Number of atoms: 8254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8254 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 47, 'TRANS': 996} Chain breaks: 6 Chain: "C" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2641 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 17, 'TRANS': 312} Chain breaks: 1 Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1337 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain breaks: 2 Chain: "I" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 393 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 54} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "P" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} Chain: "E" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1590 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 9, 'TRANS': 184} Chain breaks: 2 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: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1002 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 2 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: "O" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3546 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "Q" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 724 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 985 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1272 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain breaks: 2 Chain: "N" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 697 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain breaks: 1 Chain: "X" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 327 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "Y" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 477 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "R" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 534 SG CYS A 69 98.362 67.954 107.805 1.00 96.02 S ATOM 556 SG CYS A 72 95.640 64.640 109.497 1.00 94.46 S ATOM 604 SG CYS A 79 95.192 67.076 106.302 1.00 88.70 S ATOM 1236 SG CYS A 156 63.353 93.706 135.896 1.00118.39 S ATOM 1262 SG CYS A 159 65.469 93.250 138.719 1.00121.42 S ATOM 17993 SG CYS B1080 82.403 63.720 115.962 1.00 81.64 S ATOM 18012 SG CYS B1083 81.680 65.573 118.972 1.00 81.49 S ATOM 18078 SG CYS B1092 85.646 65.364 116.253 1.00 86.49 S ATOM 18106 SG CYS B1095 83.758 63.067 120.814 1.00 88.09 S ATOM 22417 SG CYS I 5 55.633 148.605 105.275 1.00122.02 S ATOM 22565 SG CYS I 25 57.767 146.274 109.192 1.00125.31 S ATOM 23641 SG CYS L 19 122.426 95.761 62.177 1.00 81.26 S ATOM 23803 SG CYS L 39 121.911 101.343 62.390 1.00 97.98 S ATOM 24762 SG CYS P 287 89.383 78.467 141.011 1.00121.28 S ATOM 28236 SG CYS J 7 87.230 83.024 39.029 1.00 54.01 S ATOM 28260 SG CYS J 10 84.149 79.831 36.303 1.00 57.92 S ATOM 28524 SG CYS J 44 84.058 83.310 37.338 1.00 57.10 S ATOM 28530 SG CYS J 45 87.080 83.108 35.453 1.00 54.89 S Time building chain proxies: 18.80, per 1000 atoms: 0.51 Number of scatterers: 36856 At special positions: 0 Unit cell: (138.86, 183.38, 192.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 249 16.00 P 45 15.00 Mg 1 11.99 O 6928 8.00 N 6411 7.00 C 23212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.64 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 307 " Number of angles added : 6 Zn2+ tetrahedral coordination pdb=" ZN A1902 " pdb="ZN ZN A1902 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 72 " pdb=" ZN A1903 " pdb="ZN ZN A1903 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1903 " - pdb=" SG CYS A 156 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 5 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 25 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 15 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 150 helices and 39 sheets defined 31.8% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.75 Creating SS restraints... Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 98 through 105 Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 137 through 150 removed outlier: 4.429A pdb=" N LEU A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.742A pdb=" N LEU A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 Proline residue: A 236 - end of helix No H-bonds generated for 'chain 'A' and resid 232 through 238' Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.728A pdb=" N LYS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.920A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 384 through 387 No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 543 through 552 removed outlier: 4.369A pdb=" N TYR A 550 " --> pdb=" O THR A 547 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 552 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 570 removed outlier: 3.658A pdb=" N CYS A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 570 " --> pdb=" O GLN A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 4.004A pdb=" N VAL A 603 " --> pdb=" O GLN A 599 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 674 through 694 removed outlier: 3.842A pdb=" N ARG A 685 " --> pdb=" O SER A 681 " (cutoff:3.500A) Proline residue: A 688 - end of helix removed outlier: 3.801A pdb=" N ASN A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 707 through 732 removed outlier: 3.600A pdb=" N LYS A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 723 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 731 " --> pdb=" O TYR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 770 removed outlier: 3.707A pdb=" N LYS A 754 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 761 " --> pdb=" O SER A 757 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 768 " --> pdb=" O GLY A 764 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 782 Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 844 through 876 removed outlier: 3.859A pdb=" N GLU A 856 " --> pdb=" O MET A 852 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR A 870 " --> pdb=" O ALA A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 904 No H-bonds generated for 'chain 'A' and resid 902 through 904' Processing helix chain 'A' and resid 921 through 931 Processing helix chain 'A' and resid 945 through 951 Processing helix chain 'A' and resid 966 through 986 removed outlier: 3.684A pdb=" N LYS A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 979 " --> pdb=" O GLY A 975 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1002 removed outlier: 3.552A pdb=" N TYR A1001 " --> pdb=" O ARG A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1024 removed outlier: 3.805A pdb=" N GLU A1012 " --> pdb=" O PRO A1008 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A1020 " --> pdb=" O GLU A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1046 removed outlier: 3.529A pdb=" N GLN A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) Proline residue: A1044 - end of helix Processing helix chain 'A' and resid 1067 through 1075 removed outlier: 3.591A pdb=" N GLU A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1105 Processing helix chain 'A' and resid 1111 through 1113 No H-bonds generated for 'chain 'A' and resid 1111 through 1113' Processing helix chain 'A' and resid 1134 through 1139 Processing helix chain 'A' and resid 1146 through 1153 Processing helix chain 'A' and resid 1187 through 1198 removed outlier: 4.278A pdb=" N GLU A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A1195 " --> pdb=" O PHE A1191 " (cutoff:3.500A) Proline residue: A1197 - end of helix Processing helix chain 'A' and resid 1232 through 1236 Processing helix chain 'A' and resid 1251 through 1255 Processing helix chain 'A' and resid 1261 through 1277 removed outlier: 3.501A pdb=" N ILE A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A1271 " --> pdb=" O ILE A1267 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A1274 " --> pdb=" O GLU A1270 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1294 removed outlier: 3.725A pdb=" N ASP A1292 " --> pdb=" O MET A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1309 removed outlier: 3.868A pdb=" N ALA A1309 " --> pdb=" O ARG A1305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1305 through 1309' Processing helix chain 'A' and resid 1315 through 1319 Processing helix chain 'A' and resid 1324 through 1333 removed outlier: 3.525A pdb=" N LEU A1328 " --> pdb=" O THR A1324 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A1331 " --> pdb=" O HIS A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1349 No H-bonds generated for 'chain 'A' and resid 1346 through 1349' Processing helix chain 'B' and resid 27 through 37 Proline residue: B 31 - end of helix removed outlier: 3.940A pdb=" N LEU B 34 " --> pdb=" O PRO B 31 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 35 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS B 37 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 52 removed outlier: 3.611A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.655A pdb=" N ALA B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 152 through 157' Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 266 through 275 removed outlier: 5.273A pdb=" N GLU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N CYS B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.879A pdb=" N GLY B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 314 No H-bonds generated for 'chain 'B' and resid 311 through 314' Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.640A pdb=" N ILE B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 342 " --> pdb=" O MET B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 391 removed outlier: 3.596A pdb=" N LEU B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 385 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 420 removed outlier: 3.628A pdb=" N ASP B 409 " --> pdb=" O MET B 406 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE B 411 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR B 412 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASN B 413 " --> pdb=" O GLN B 410 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B 416 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN B 417 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER B 420 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 452 removed outlier: 3.941A pdb=" N MET B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 509 through 518 removed outlier: 3.683A pdb=" N ASN B 517 " --> pdb=" O LYS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 565 Processing helix chain 'B' and resid 609 through 616 removed outlier: 3.707A pdb=" N ALA B 615 " --> pdb=" O MET B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 removed outlier: 3.677A pdb=" N LEU B 625 " --> pdb=" O PHE B 621 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 621 through 626' Processing helix chain 'B' and resid 637 through 640 Processing helix chain 'B' and resid 661 through 664 removed outlier: 3.910A pdb=" N LEU B 664 " --> pdb=" O PRO B 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 661 through 664' Processing helix chain 'B' and resid 680 through 691 removed outlier: 3.639A pdb=" N THR B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR B 685 " --> pdb=" O PRO B 681 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 688 " --> pdb=" O THR B 684 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 727 No H-bonds generated for 'chain 'B' and resid 724 through 727' Processing helix chain 'B' and resid 761 through 764 No H-bonds generated for 'chain 'B' and resid 761 through 764' Processing helix chain 'B' and resid 913 through 915 No H-bonds generated for 'chain 'B' and resid 913 through 915' Processing helix chain 'B' and resid 931 through 937 removed outlier: 3.613A pdb=" N PHE B 934 " --> pdb=" O PRO B 931 " (cutoff:3.500A) Proline residue: B 935 - end of helix No H-bonds generated for 'chain 'B' and resid 931 through 937' Processing helix chain 'B' and resid 940 through 955 removed outlier: 3.791A pdb=" N LEU B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 950 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 954 " --> pdb=" O LYS B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 976 removed outlier: 4.458A pdb=" N GLU B 974 " --> pdb=" O LYS B 970 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B 975 " --> pdb=" O ASP B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1018 No H-bonds generated for 'chain 'B' and resid 1016 through 1018' Processing helix chain 'B' and resid 1049 through 1057 removed outlier: 3.550A pdb=" N CYS B1054 " --> pdb=" O MET B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1068 Processing helix chain 'B' and resid 1108 through 1117 Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 73 through 82 removed outlier: 3.525A pdb=" N ARG C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 109 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 256 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' 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 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 318 through 342 removed outlier: 3.924A pdb=" N SER C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 33 removed outlier: 3.751A pdb=" N ALA G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU G 29 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS G 32 " --> pdb=" O GLU G 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 60 removed outlier: 4.218A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR K 57 " --> pdb=" O ASN K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 125 removed outlier: 3.781A pdb=" N ASN K 101 " --> pdb=" O GLN K 97 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER K 117 " --> pdb=" O LYS K 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 205 No H-bonds generated for 'chain 'P' and resid 202 through 205' Processing helix chain 'P' and resid 220 through 227 Processing helix chain 'P' and resid 242 through 254 removed outlier: 4.826A pdb=" N LYS P 247 " --> pdb=" O ILE P 243 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL P 248 " --> pdb=" O TYR P 244 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU P 249 " --> pdb=" O ASP P 245 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET P 250 " --> pdb=" O GLY P 246 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA P 254 " --> pdb=" O MET P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 286 through 289 No H-bonds generated for 'chain 'P' and resid 286 through 289' Processing helix chain 'P' and resid 292 through 294 No H-bonds generated for 'chain 'P' and resid 292 through 294' Processing helix chain 'P' and resid 304 through 306 No H-bonds generated for 'chain 'P' and resid 304 through 306' Processing helix chain 'P' and resid 308 through 313 Processing helix chain 'E' and resid 12 through 23 removed outlier: 4.010A pdb=" N HIS E 22 " --> pdb=" O MET E 18 " (cutoff:3.500A) 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 40 No H-bonds generated for 'chain 'E' and resid 37 through 40' Processing helix chain 'E' and resid 44 through 48 Proline residue: E 48 - end of helix No H-bonds generated for 'chain 'E' and resid 44 through 48' Processing helix chain 'E' and resid 84 through 96 removed outlier: 3.958A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 120 removed outlier: 3.624A pdb=" N LEU E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 135 No H-bonds generated for 'chain 'E' and resid 132 through 135' Processing helix chain 'E' and resid 153 through 163 removed outlier: 3.674A pdb=" N THR E 157 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 75 removed outlier: 3.545A pdb=" N ARG F 64 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 98 removed outlier: 3.503A pdb=" N LYS F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 17 No H-bonds generated for 'chain 'J' and resid 15 through 17' Processing helix chain 'J' and resid 19 through 26 Processing helix chain 'J' and resid 31 through 37 removed outlier: 4.257A pdb=" N LEU J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 50 No H-bonds generated for 'chain 'J' and resid 47 through 50' Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.981A pdb=" N LEU J 59 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU J 60 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 16 removed outlier: 3.527A pdb=" N GLN O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 31 Processing helix chain 'O' and resid 36 through 42 Processing helix chain 'O' and resid 47 through 59 Processing helix chain 'O' and resid 79 through 97 removed outlier: 3.899A pdb=" N LEU O 83 " --> pdb=" O CYS O 79 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG O 84 " --> pdb=" O SER O 80 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU O 86 " --> pdb=" O VAL O 82 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) Proline residue: O 89 - end of helix removed outlier: 3.543A pdb=" N THR O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR O 95 " --> pdb=" O TYR O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 112 Processing helix chain 'O' and resid 118 through 132 removed outlier: 4.284A pdb=" N LYS O 123 " --> pdb=" O SER O 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP O 127 " --> pdb=" O LYS O 123 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR O 130 " --> pdb=" O ALA O 126 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 153 removed outlier: 3.571A pdb=" N VAL O 149 " --> pdb=" O SER O 145 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA O 152 " --> pdb=" O PHE O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 174 No H-bonds generated for 'chain 'O' and resid 171 through 174' Processing helix chain 'O' and resid 239 through 256 Processing helix chain 'O' and resid 261 through 272 removed outlier: 3.597A pdb=" N GLU O 265 " --> pdb=" O GLN O 261 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE O 266 " --> pdb=" O THR O 262 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL O 267 " --> pdb=" O SER O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 295 Processing helix chain 'O' and resid 305 through 316 Processing helix chain 'O' and resid 338 through 357 removed outlier: 3.678A pdb=" N LEU O 342 " --> pdb=" O LEU O 338 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR O 347 " --> pdb=" O ALA O 343 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 371 removed outlier: 3.538A pdb=" N ILE O 365 " --> pdb=" O ARG O 361 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU O 368 " --> pdb=" O ARG O 364 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL O 369 " --> pdb=" O ILE O 365 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU O 370 " --> pdb=" O PHE O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 383 No H-bonds generated for 'chain 'O' and resid 380 through 383' Processing helix chain 'O' and resid 388 through 400 removed outlier: 3.652A pdb=" N ASP O 393 " --> pdb=" O LYS O 389 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET O 394 " --> pdb=" O GLU O 390 " (cutoff:3.500A) Processing helix chain 'O' and resid 428 through 455 removed outlier: 3.622A pdb=" N LEU O 435 " --> pdb=" O ALA O 431 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA O 444 " --> pdb=" O TYR O 440 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG O 449 " --> pdb=" O ASN O 445 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR O 454 " --> pdb=" O ARG O 450 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS O 455 " --> pdb=" O GLN O 451 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 464 removed outlier: 3.738A pdb=" N LEU O 461 " --> pdb=" O LYS O 458 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU O 462 " --> pdb=" O ARG O 459 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS O 463 " --> pdb=" O LEU O 460 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER O 464 " --> pdb=" O LEU O 461 " (cutoff:3.500A) Processing helix chain 'O' and resid 493 through 515 removed outlier: 3.653A pdb=" N LEU O 499 " --> pdb=" O GLU O 495 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE O 514 " --> pdb=" O ASP O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 517 through 530 removed outlier: 3.986A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 61 removed outlier: 3.780A pdb=" N THR Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY Q 51 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU Q 52 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU Q 54 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET Q 57 " --> pdb=" O GLU Q 54 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU Q 58 " --> pdb=" O GLU Q 55 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS Q 61 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 76 Processing helix chain 'D' and resid 13 through 30 removed outlier: 3.525A pdb=" N LYS D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER D 30 " --> pdb=" O GLN D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 41 through 55 removed outlier: 3.664A pdb=" N LYS D 51 " --> pdb=" O TYR D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 76 removed outlier: 3.522A pdb=" N ALA D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'M' and resid 70 through 76 Processing helix chain 'M' and resid 141 through 151 Processing helix chain 'N' and resid 253 through 260 Processing helix chain 'N' and resid 342 through 344 No H-bonds generated for 'chain 'N' and resid 342 through 344' Processing sheet with id= A, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= B, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.888A pdb=" N GLY A 84 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 364 through 368 removed outlier: 4.092A pdb=" N THR A 367 " --> pdb=" O MET A 505 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 458 " --> pdb=" O ALA A 478 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 369 through 371 removed outlier: 5.889A pdb=" N PHE A 486 " --> pdb=" O SER A 370 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 391 through 395 Processing sheet with id= F, first strand: chain 'A' and resid 617 through 620 Processing sheet with id= G, first strand: chain 'A' and resid 1084 through 1088 Processing sheet with id= H, first strand: chain 'A' and resid 1118 through 1122 removed outlier: 3.639A pdb=" N LEU A1122 " --> pdb=" O ASP A1125 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1166 through 1168 removed outlier: 3.829A pdb=" N VAL A1173 " --> pdb=" O HIS A1168 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 110 through 113 removed outlier: 3.525A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 169 through 171 Processing sheet with id= L, first strand: chain 'B' and resid 181 through 184 Processing sheet with id= M, first strand: chain 'B' and resid 189 through 191 removed outlier: 4.094A pdb=" N ILE B 190 " --> pdb=" O GLY B 200 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA B 201 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 538 through 541 Processing sheet with id= O, first strand: chain 'B' and resid 593 through 597 Processing sheet with id= P, first strand: chain 'B' and resid 709 through 712 Processing sheet with id= Q, first strand: chain 'B' and resid 739 through 741 Processing sheet with id= R, first strand: chain 'B' and resid 1075 through 1080 removed outlier: 3.630A pdb=" N ILE B1106 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B1077 " --> pdb=" O LEU B1104 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 755 through 758 removed outlier: 7.275A pdb=" N LEU B 757 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE B 910 " --> pdb=" O LEU B 757 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 825 through 828 removed outlier: 4.063A pdb=" N GLN B 825 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 865 through 872 removed outlier: 6.705A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 13 through 15 removed outlier: 3.534A pdb=" N ARG C 298 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 173 through 176 removed outlier: 4.457A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS C 146 " --> pdb=" O GLN C 206 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN C 206 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 233 through 235 Processing sheet with id= Y, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.571A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 3 through 13 Processing sheet with id= AA, first strand: chain 'G' and resid 37 through 39 removed outlier: 3.988A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 83 through 87 removed outlier: 4.797A pdb=" N GLU G 83 " --> pdb=" O PHE G 150 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE G 150 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER G 189 " --> pdb=" O ARG G 151 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'K' and resid 39 through 45 Processing sheet with id= AD, first strand: chain 'E' and resid 103 through 105 removed outlier: 6.941A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.820A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AG, first strand: chain 'H' and resid 39 through 44 removed outlier: 3.648A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 139 through 142 removed outlier: 4.221A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU H 125 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.674A pdb=" N GLN O 66 " --> pdb=" O GLU O 74 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU O 74 " --> pdb=" O GLN O 66 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 14 through 16 Processing sheet with id= AK, first strand: chain 'N' and resid 268 through 270 Processing sheet with id= AL, first strand: chain 'N' and resid 328 through 331 removed outlier: 3.685A pdb=" N LYS N 328 " --> pdb=" O LEU N 340 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL N 337 " --> pdb=" O THR N 349 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR N 349 " --> pdb=" O VAL N 337 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'N' and resid 362 through 365 removed outlier: 6.063A pdb=" N GLY N 364 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N VAL N 375 " --> pdb=" O GLY N 364 " (cutoff:3.500A) 857 hydrogen bonds defined for protein. 2415 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.54 Time building geometry restraints manager: 14.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 13668 1.37 - 1.56: 23467 1.56 - 1.76: 92 1.76 - 1.95: 378 1.95 - 2.14: 12 Bond restraints: 37617 Sorted by residual: bond pdb=" C PRO I 29 " pdb=" O PRO I 29 " ideal model delta sigma weight residual 1.235 1.184 0.051 7.90e-03 1.60e+04 4.20e+01 bond pdb=" CA GLN B 692 " pdb=" C GLN B 692 " ideal model delta sigma weight residual 1.523 1.445 0.078 1.41e-02 5.03e+03 3.05e+01 bond pdb=" N LEU M 45 " pdb=" CA LEU M 45 " ideal model delta sigma weight residual 1.458 1.492 -0.033 6.30e-03 2.52e+04 2.82e+01 bond pdb=" CA TYR B 357 " pdb=" C TYR B 357 " ideal model delta sigma weight residual 1.523 1.447 0.076 1.56e-02 4.11e+03 2.40e+01 bond pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 2.280 2.134 0.146 3.00e-02 1.11e+03 2.38e+01 ... (remaining 37612 not shown) Histogram of bond angle deviations from ideal: 89.47 - 98.62: 36 98.62 - 107.77: 2463 107.77 - 116.92: 24402 116.92 - 126.08: 23465 126.08 - 135.23: 590 Bond angle restraints: 50956 Sorted by residual: angle pdb="FE3 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.51 -16.81 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE2 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.51 -16.81 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE3 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.48 -16.78 1.50e+00 4.44e-01 1.25e+02 angle pdb="FE2 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.48 -16.78 1.50e+00 4.44e-01 1.25e+02 angle pdb=" N ARG A 59 " pdb=" CA ARG A 59 " pdb=" C ARG A 59 " ideal model delta sigma weight residual 113.38 99.70 13.68 1.23e+00 6.61e-01 1.24e+02 ... (remaining 50951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 22161 35.52 - 71.04: 782 71.04 - 106.56: 32 106.56 - 142.08: 0 142.08 - 177.59: 1 Dihedral angle restraints: 22976 sinusoidal: 9833 harmonic: 13143 Sorted by residual: dihedral pdb=" C LEU B 809 " pdb=" N LEU B 809 " pdb=" CA LEU B 809 " pdb=" CB LEU B 809 " ideal model delta harmonic sigma weight residual -122.60 -145.70 23.10 0 2.50e+00 1.60e-01 8.53e+01 dihedral pdb=" N LEU B 809 " pdb=" C LEU B 809 " pdb=" CA LEU B 809 " pdb=" CB LEU B 809 " ideal model delta harmonic sigma weight residual 122.80 145.46 -22.66 0 2.50e+00 1.60e-01 8.21e+01 dihedral pdb=" C ILE M 77 " pdb=" N ILE M 77 " pdb=" CA ILE M 77 " pdb=" CB ILE M 77 " ideal model delta harmonic sigma weight residual -122.00 -141.35 19.35 0 2.50e+00 1.60e-01 5.99e+01 ... (remaining 22973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 5507 0.194 - 0.389: 226 0.389 - 0.583: 22 0.583 - 0.778: 1 0.778 - 0.972: 5 Chirality restraints: 5761 Sorted by residual: chirality pdb=" CA LEU B 809 " pdb=" N LEU B 809 " pdb=" C LEU B 809 " pdb=" CB LEU B 809 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.36e+01 chirality pdb="FE4 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb=" S3 SF4 P 401 " both_signs ideal model delta sigma weight residual False 10.55 9.72 0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb="FE1 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb=" S4 SF4 P 401 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.83 2.00e-01 2.50e+01 1.71e+01 ... (remaining 5758 not shown) Planarity restraints: 6377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 162 " 0.024 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C LEU C 162 " -0.083 2.00e-02 2.50e+03 pdb=" O LEU C 162 " 0.031 2.00e-02 2.50e+03 pdb=" N TYR C 163 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1111 " -0.023 2.00e-02 2.50e+03 4.70e-02 2.21e+01 pdb=" C GLY A1111 " 0.081 2.00e-02 2.50e+03 pdb=" O GLY A1111 " -0.030 2.00e-02 2.50e+03 pdb=" N GLU A1112 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 617 " 0.022 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C GLY B 617 " -0.080 2.00e-02 2.50e+03 pdb=" O GLY B 617 " 0.031 2.00e-02 2.50e+03 pdb=" N TYR B 618 " 0.027 2.00e-02 2.50e+03 ... (remaining 6374 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 484 2.55 - 3.14: 29185 3.14 - 3.72: 59008 3.72 - 4.31: 82139 4.31 - 4.90: 132528 Nonbonded interactions: 303344 Sorted by model distance: nonbonded pdb=" O3' U R 9 " pdb="MG MG A1901 " model vdw 1.961 2.170 nonbonded pdb=" N ASP C 183 " pdb=" OD1 ASP C 183 " model vdw 2.073 2.520 nonbonded pdb=" O ALA A 161 " pdb="ZN ZN A1903 " model vdw 2.102 2.230 nonbonded pdb=" O THR M 107 " pdb=" OG1 THR M 107 " model vdw 2.133 2.440 nonbonded pdb=" CD2 LEU N 357 " pdb=" NE2 GLN N 358 " model vdw 2.145 3.540 ... (remaining 303339 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.040 Extract box with map and model: 8.580 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 101.840 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 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 : 0.012 0.146 37617 Z= 0.784 Angle : 1.428 16.811 50956 Z= 0.910 Chirality : 0.092 0.972 5761 Planarity : 0.008 0.080 6377 Dihedral : 17.046 177.595 14472 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.89 % Favored : 89.43 % Rotamer: Outliers : 4.73 % Allowed : 13.28 % Favored : 81.99 % Cbeta Deviations : 0.73 % 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: -4.77 (0.10), residues: 4437 helix: -3.86 (0.08), residues: 1495 sheet: -2.92 (0.20), residues: 506 loop : -2.77 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP P 217 HIS 0.013 0.002 HIS A 82 PHE 0.036 0.003 PHE B 662 TYR 0.043 0.003 TYR M 114 ARG 0.013 0.001 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1133 time to evaluate : 4.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 VAL cc_start: 0.8869 (t) cc_final: 0.8586 (p) REVERT: A 313 LEU cc_start: 0.8882 (tt) cc_final: 0.8641 (tt) REVERT: A 1190 GLN cc_start: 0.8311 (tp40) cc_final: 0.8033 (tp40) REVERT: B 317 ILE cc_start: 0.8322 (mm) cc_final: 0.7956 (tp) REVERT: B 521 GLU cc_start: 0.3960 (OUTLIER) cc_final: 0.3249 (tp30) REVERT: B 527 CYS cc_start: 0.6797 (m) cc_final: 0.6346 (m) REVERT: B 574 ILE cc_start: 0.6489 (OUTLIER) cc_final: 0.6242 (tt) REVERT: B 634 ASP cc_start: 0.5770 (p0) cc_final: 0.5484 (p0) REVERT: B 769 CYS cc_start: 0.4529 (m) cc_final: 0.4229 (m) REVERT: B 869 VAL cc_start: 0.6298 (OUTLIER) cc_final: 0.5801 (p) REVERT: C 87 MET cc_start: 0.6806 (mmm) cc_final: 0.6484 (mmm) REVERT: K 39 CYS cc_start: 0.5760 (p) cc_final: 0.5051 (p) REVERT: E 37 LEU cc_start: 0.7414 (tp) cc_final: 0.6877 (tp) REVERT: E 110 MET cc_start: 0.5770 (mtp) cc_final: 0.5526 (ttm) REVERT: O 41 HIS cc_start: 0.7706 (m90) cc_final: 0.7421 (m-70) REVERT: O 72 VAL cc_start: 0.7499 (t) cc_final: 0.6971 (p) REVERT: O 118 MET cc_start: 0.7129 (ttm) cc_final: 0.6357 (ttt) REVERT: O 415 HIS cc_start: 0.6927 (m-70) cc_final: 0.6637 (m170) REVERT: O 448 GLU cc_start: 0.8738 (tp30) cc_final: 0.8418 (pp20) REVERT: Q 32 LEU cc_start: 0.6495 (mt) cc_final: 0.5885 (pp) REVERT: Q 54 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8033 (tm-30) REVERT: N 360 LEU cc_start: 0.3914 (OUTLIER) cc_final: 0.3461 (tt) outliers start: 188 outliers final: 48 residues processed: 1248 average time/residue: 0.5271 time to fit residues: 1026.4461 Evaluate side-chains 648 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 596 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 1099 ARG Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain P residue 284 ARG Chi-restraints excluded: chain O residue 409 ILE Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 193 TYR Chi-restraints excluded: chain N residue 329 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain N residue 375 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 379 optimal weight: 1.9990 chunk 340 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 229 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 213 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 chunk 407 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN A 374 ASN A 422 GLN A 511 GLN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN ** A 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 608 ASN B 639 ASN B 692 GLN B 806 HIS B 825 GLN ** B 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 181 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN L 23 HIS L 26 ASN ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 274 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN E 132 GLN O 14 GLN O 16 HIS O 49 GLN O 113 ASN O 261 GLN O 337 ASN O 377 GLN O 379 GLN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 415 HIS ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 457 ASN O 465 GLN O 497 GLN O 507 ASN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 ASN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 37617 Z= 0.265 Angle : 0.852 16.550 50956 Z= 0.429 Chirality : 0.048 0.257 5761 Planarity : 0.006 0.091 6377 Dihedral : 12.318 178.940 5531 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.43 % Favored : 91.35 % Rotamer: Outliers : 4.93 % Allowed : 19.72 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.02 % 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: -3.77 (0.11), residues: 4437 helix: -2.34 (0.11), residues: 1542 sheet: -2.73 (0.20), residues: 516 loop : -2.57 (0.11), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP G 201 HIS 0.011 0.002 HIS O 60 PHE 0.032 0.002 PHE G 18 TYR 0.020 0.002 TYR D 14 ARG 0.010 0.001 ARG A1233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 661 time to evaluate : 3.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 MET cc_start: 0.7876 (mmt) cc_final: 0.7157 (mpp) REVERT: B 254 MET cc_start: 0.7576 (mmt) cc_final: 0.7085 (mmt) REVERT: B 1062 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7689 (mpp) REVERT: B 1126 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8441 (mt) REVERT: C 87 MET cc_start: 0.7349 (mmm) cc_final: 0.7075 (mmt) REVERT: G 37 LYS cc_start: 0.7132 (mmmm) cc_final: 0.6929 (mmmm) REVERT: G 190 ILE cc_start: 0.6253 (mp) cc_final: 0.5897 (mt) REVERT: K 70 TYR cc_start: 0.7805 (p90) cc_final: 0.7550 (p90) REVERT: P 205 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.6915 (pp30) REVERT: P 232 MET cc_start: 0.5345 (mmp) cc_final: 0.5054 (mmp) REVERT: E 121 MET cc_start: 0.7695 (tmm) cc_final: 0.7082 (tmm) REVERT: O 72 VAL cc_start: 0.7540 (t) cc_final: 0.7161 (p) REVERT: O 404 MET cc_start: 0.6995 (mmm) cc_final: 0.6724 (mmp) REVERT: O 448 GLU cc_start: 0.8939 (tp30) cc_final: 0.8265 (pp20) REVERT: Q 29 ASP cc_start: 0.7976 (p0) cc_final: 0.7713 (p0) REVERT: Q 54 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8210 (tm-30) REVERT: Q 84 ILE cc_start: 0.4408 (mt) cc_final: 0.4072 (mt) REVERT: Q 111 MET cc_start: 0.6706 (mmm) cc_final: 0.6283 (tmm) REVERT: D 41 ASN cc_start: 0.5471 (m-40) cc_final: 0.5266 (t0) REVERT: N 352 THR cc_start: 0.2648 (OUTLIER) cc_final: 0.2257 (p) REVERT: N 363 VAL cc_start: 0.4043 (t) cc_final: 0.3694 (t) outliers start: 196 outliers final: 89 residues processed: 799 average time/residue: 0.4876 time to fit residues: 633.2103 Evaluate side-chains 621 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 528 time to evaluate : 3.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1062 MET Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 219 TYR Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 409 ILE Chi-restraints excluded: chain O residue 445 ASN Chi-restraints excluded: chain O residue 530 THR Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 352 THR Chi-restraints excluded: chain N residue 375 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 226 optimal weight: 10.0000 chunk 126 optimal weight: 0.0370 chunk 339 optimal weight: 8.9990 chunk 277 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 408 optimal weight: 20.0000 chunk 441 optimal weight: 20.0000 chunk 363 optimal weight: 9.9990 chunk 405 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 327 optimal weight: 0.4980 overall best weight: 1.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 693 ASN A 794 GLN A 815 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS B 280 GLN B 289 ASN B 887 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS L 26 ASN ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 37617 Z= 0.256 Angle : 0.754 13.211 50956 Z= 0.381 Chirality : 0.046 0.284 5761 Planarity : 0.005 0.088 6377 Dihedral : 11.508 176.539 5463 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.72 % Favored : 91.08 % Rotamer: Outliers : 4.15 % Allowed : 21.38 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -3.06 (0.11), residues: 4437 helix: -1.37 (0.12), residues: 1536 sheet: -2.48 (0.20), residues: 518 loop : -2.41 (0.12), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 201 HIS 0.017 0.001 HIS M 200 PHE 0.034 0.002 PHE B 559 TYR 0.022 0.002 TYR O 424 ARG 0.010 0.001 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 582 time to evaluate : 4.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 GLU cc_start: 0.8054 (pt0) cc_final: 0.7546 (pt0) REVERT: A 440 MET cc_start: 0.8039 (mmt) cc_final: 0.7345 (mpp) REVERT: A 1244 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8411 (p) REVERT: B 139 MET cc_start: 0.6306 (ttp) cc_final: 0.5739 (ptm) REVERT: B 254 MET cc_start: 0.7447 (mmt) cc_final: 0.6964 (mmt) REVERT: B 272 CYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7420 (m) REVERT: B 317 ILE cc_start: 0.8433 (tp) cc_final: 0.8214 (tp) REVERT: B 341 ARG cc_start: 0.7747 (mmt90) cc_final: 0.7513 (mpt180) REVERT: B 431 MET cc_start: 0.7753 (ppp) cc_final: 0.7550 (ppp) REVERT: B 527 CYS cc_start: 0.6388 (m) cc_final: 0.5933 (m) REVERT: B 916 MET cc_start: 0.7329 (ttm) cc_final: 0.7105 (tpp) REVERT: C 10 MET cc_start: 0.7247 (mmm) cc_final: 0.7023 (mmm) REVERT: C 81 LEU cc_start: 0.8740 (tp) cc_final: 0.8422 (mp) REVERT: C 87 MET cc_start: 0.7744 (mmm) cc_final: 0.7289 (mmm) REVERT: G 190 ILE cc_start: 0.6565 (mp) cc_final: 0.6096 (mt) REVERT: K 70 TYR cc_start: 0.8119 (p90) cc_final: 0.7826 (p90) REVERT: L 48 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7835 (ttm-80) REVERT: P 232 MET cc_start: 0.5393 (mmp) cc_final: 0.5029 (mmp) REVERT: F 83 LEU cc_start: 0.8903 (pt) cc_final: 0.8660 (pp) REVERT: J 17 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7617 (mmtm) REVERT: O 60 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.7496 (m-70) REVERT: O 513 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6831 (mt-10) REVERT: Q 29 ASP cc_start: 0.8307 (p0) cc_final: 0.7931 (p0) REVERT: Q 54 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8064 (tm-30) REVERT: Q 111 MET cc_start: 0.6678 (mmm) cc_final: 0.6202 (tmm) REVERT: N 363 VAL cc_start: 0.4763 (t) cc_final: 0.4071 (t) outliers start: 165 outliers final: 85 residues processed: 708 average time/residue: 0.4696 time to fit residues: 542.1548 Evaluate side-chains 595 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 506 time to evaluate : 4.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1122 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 409 ILE Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 365 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 403 optimal weight: 0.9980 chunk 307 optimal weight: 8.9990 chunk 211 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 274 optimal weight: 20.0000 chunk 409 optimal weight: 0.9980 chunk 434 optimal weight: 0.1980 chunk 214 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A1039 GLN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 ASN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 407 GLN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 ASN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 HIS M 106 GLN M 121 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37617 Z= 0.200 Angle : 0.720 13.543 50956 Z= 0.355 Chirality : 0.045 0.344 5761 Planarity : 0.005 0.087 6377 Dihedral : 11.172 178.359 5449 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.36 % Favored : 91.44 % Rotamer: Outliers : 3.62 % Allowed : 22.59 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.12), residues: 4437 helix: -0.98 (0.13), residues: 1538 sheet: -2.28 (0.21), residues: 506 loop : -2.23 (0.12), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 40 HIS 0.010 0.001 HIS M 130 PHE 0.022 0.001 PHE G 120 TYR 0.018 0.001 TYR H 48 ARG 0.007 0.000 ARG M 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 552 time to evaluate : 4.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 MET cc_start: 0.8020 (mmt) cc_final: 0.6878 (mpp) REVERT: A 843 THR cc_start: 0.7557 (OUTLIER) cc_final: 0.7354 (t) REVERT: B 139 MET cc_start: 0.6568 (ttp) cc_final: 0.6177 (ptm) REVERT: B 272 CYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7358 (m) REVERT: B 317 ILE cc_start: 0.8331 (tp) cc_final: 0.8101 (tp) REVERT: B 697 ILE cc_start: 0.8180 (tp) cc_final: 0.7836 (mp) REVERT: B 886 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.6898 (mtm110) REVERT: C 81 LEU cc_start: 0.8670 (tp) cc_final: 0.8371 (mp) REVERT: G 190 ILE cc_start: 0.6216 (mp) cc_final: 0.5847 (mp) REVERT: K 70 TYR cc_start: 0.8180 (p90) cc_final: 0.7848 (p90) REVERT: L 48 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7808 (ttm-80) REVERT: P 232 MET cc_start: 0.5284 (mmp) cc_final: 0.4937 (mmp) REVERT: O 404 MET cc_start: 0.8209 (mmp) cc_final: 0.7843 (mmm) REVERT: O 427 ASN cc_start: 0.7600 (t0) cc_final: 0.6935 (t0) REVERT: O 448 GLU cc_start: 0.8992 (tp30) cc_final: 0.8362 (pp20) REVERT: Q 54 GLU cc_start: 0.8924 (mm-30) cc_final: 0.7974 (tm-30) REVERT: Q 86 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.5905 (ptm160) REVERT: Q 111 MET cc_start: 0.6717 (mmm) cc_final: 0.6441 (tmm) REVERT: N 363 VAL cc_start: 0.5364 (t) cc_final: 0.4905 (t) outliers start: 144 outliers final: 90 residues processed: 658 average time/residue: 0.5052 time to fit residues: 549.8353 Evaluate side-chains 584 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 489 time to evaluate : 3.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 886 ARG Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 266 HIS Chi-restraints excluded: chain P residue 270 TYR Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 409 ILE Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 345 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 361 optimal weight: 0.7980 chunk 246 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 323 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 370 optimal weight: 10.0000 chunk 300 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 389 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 HIS ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN B 703 ASN ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 HIS ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 HIS ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 297 HIS ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN ** O 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 112 GLN M 121 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.7003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.188 37617 Z= 0.438 Angle : 0.871 11.739 50956 Z= 0.443 Chirality : 0.049 0.285 5761 Planarity : 0.006 0.090 6377 Dihedral : 11.172 175.664 5442 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.49 % Favored : 90.31 % Rotamer: Outliers : 5.46 % Allowed : 22.69 % Favored : 71.86 % Cbeta Deviations : 0.00 % 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: -2.48 (0.12), residues: 4437 helix: -0.74 (0.13), residues: 1504 sheet: -2.34 (0.21), residues: 526 loop : -2.11 (0.12), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 18 HIS 0.011 0.002 HIS A 483 PHE 0.031 0.002 PHE C 45 TYR 0.033 0.002 TYR D 52 ARG 0.064 0.001 ARG P 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 481 time to evaluate : 4.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 GLU cc_start: 0.8314 (pt0) cc_final: 0.7950 (pt0) REVERT: A 440 MET cc_start: 0.8457 (mmt) cc_final: 0.8076 (mmm) REVERT: A 463 ASN cc_start: 0.8026 (t0) cc_final: 0.7784 (t0) REVERT: A 523 MET cc_start: 0.7777 (pmm) cc_final: 0.7307 (pmm) REVERT: B 272 CYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7449 (m) REVERT: B 281 MET cc_start: 0.8423 (ptm) cc_final: 0.8023 (ptp) REVERT: B 600 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6191 (ptmm) REVERT: B 697 ILE cc_start: 0.8755 (tp) cc_final: 0.8379 (mm) REVERT: B 886 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7200 (mtm110) REVERT: C 279 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8273 (mtp-110) REVERT: G 36 ASN cc_start: 0.6450 (m-40) cc_final: 0.5516 (m110) REVERT: G 98 HIS cc_start: 0.8508 (m-70) cc_final: 0.8299 (m-70) REVERT: K 70 TYR cc_start: 0.8437 (p90) cc_final: 0.8067 (p90) REVERT: L 48 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7759 (ttm-80) REVERT: P 193 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: P 252 ILE cc_start: 0.8920 (pt) cc_final: 0.8656 (pt) REVERT: O 9 CYS cc_start: 0.8307 (m) cc_final: 0.8041 (m) REVERT: O 267 VAL cc_start: 0.9349 (t) cc_final: 0.9065 (p) REVERT: O 404 MET cc_start: 0.8556 (mmp) cc_final: 0.8131 (mmm) REVERT: O 427 ASN cc_start: 0.8145 (t0) cc_final: 0.7534 (t0) REVERT: Q 54 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8036 (tm-30) REVERT: Q 61 LYS cc_start: 0.8174 (mmmm) cc_final: 0.7880 (tppt) REVERT: Q 111 MET cc_start: 0.7107 (mmm) cc_final: 0.6800 (tmm) REVERT: D 89 HIS cc_start: 0.4331 (OUTLIER) cc_final: 0.3987 (t-90) outliers start: 217 outliers final: 121 residues processed: 643 average time/residue: 0.5101 time to fit residues: 539.8386 Evaluate side-chains 540 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 412 time to evaluate : 4.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1194 GLU Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 886 ARG Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 259 THR Chi-restraints excluded: chain P residue 266 HIS Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 415 HIS Chi-restraints excluded: chain O residue 530 THR Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 375 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 146 optimal weight: 1.9990 chunk 390 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 254 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 434 optimal weight: 4.9990 chunk 360 optimal weight: 0.9990 chunk 201 optimal weight: 0.8980 chunk 36 optimal weight: 0.0170 chunk 143 optimal weight: 10.0000 chunk 228 optimal weight: 0.1980 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN B 253 GLN B 535 ASN B 703 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 HIS C 181 GLN I 10 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN E 132 GLN O 68 HIS O 402 ASN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 507 ASN D 26 GLN D 76 HIS M 54 GLN M 76 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.7199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37617 Z= 0.201 Angle : 0.732 13.078 50956 Z= 0.358 Chirality : 0.045 0.301 5761 Planarity : 0.005 0.092 6377 Dihedral : 11.011 179.077 5440 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.18 % Favored : 91.62 % Rotamer: Outliers : 3.77 % Allowed : 24.50 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.12), residues: 4437 helix: -0.37 (0.13), residues: 1518 sheet: -2.09 (0.22), residues: 515 loop : -1.97 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 804 HIS 0.019 0.001 HIS M 149 PHE 0.036 0.002 PHE C 185 TYR 0.020 0.001 TYR B1003 ARG 0.026 0.001 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 479 time to evaluate : 4.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7498 (p0) REVERT: A 308 GLU cc_start: 0.8191 (pt0) cc_final: 0.7630 (pt0) REVERT: A 523 MET cc_start: 0.7613 (pmm) cc_final: 0.7339 (pmm) REVERT: A 1023 MET cc_start: 0.8237 (mmm) cc_final: 0.7994 (mmt) REVERT: A 1061 MET cc_start: 0.6319 (pmm) cc_final: 0.6082 (pmm) REVERT: B 254 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7216 (mmt) REVERT: B 272 CYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7515 (m) REVERT: B 527 CYS cc_start: 0.6766 (m) cc_final: 0.5976 (m) REVERT: B 634 ASP cc_start: 0.6321 (p0) cc_final: 0.6025 (p0) REVERT: B 697 ILE cc_start: 0.8794 (tp) cc_final: 0.8479 (mp) REVERT: B 886 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.6944 (mtm110) REVERT: B 945 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6889 (mm-30) REVERT: K 70 TYR cc_start: 0.8257 (p90) cc_final: 0.8056 (p90) REVERT: L 34 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8258 (mp) REVERT: L 48 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7649 (ttm-80) REVERT: P 232 MET cc_start: 0.5898 (mmp) cc_final: 0.5585 (mmp) REVERT: O 118 MET cc_start: 0.7956 (tmm) cc_final: 0.7335 (tpt) REVERT: O 404 MET cc_start: 0.8447 (mmp) cc_final: 0.8168 (mmm) REVERT: O 427 ASN cc_start: 0.8056 (t0) cc_final: 0.7356 (t0) REVERT: Q 54 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8043 (tm-30) REVERT: Q 110 MET cc_start: 0.6760 (tmm) cc_final: 0.6253 (tmm) REVERT: Q 111 MET cc_start: 0.6917 (mmm) cc_final: 0.6615 (tmm) outliers start: 150 outliers final: 90 residues processed: 600 average time/residue: 0.4608 time to fit residues: 457.4036 Evaluate side-chains 527 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 431 time to evaluate : 4.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 787 PHE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 886 ARG Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 266 HIS Chi-restraints excluded: chain P residue 270 TYR Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 395 LEU Chi-restraints excluded: chain O residue 415 HIS Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 375 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 418 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 247 optimal weight: 8.9990 chunk 317 optimal weight: 3.9990 chunk 245 optimal weight: 0.0040 chunk 365 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 432 optimal weight: 9.9990 chunk 270 optimal weight: 7.9990 chunk 263 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 overall best weight: 4.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A1047 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 HIS M 54 GLN M 66 ASN M 121 GLN M 207 HIS ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.8095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 37617 Z= 0.379 Angle : 0.812 14.733 50956 Z= 0.408 Chirality : 0.047 0.413 5761 Planarity : 0.005 0.093 6377 Dihedral : 10.976 178.106 5437 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.58 % Favored : 90.22 % Rotamer: Outliers : 4.33 % Allowed : 24.85 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.12), residues: 4437 helix: -0.31 (0.13), residues: 1512 sheet: -2.26 (0.21), residues: 529 loop : -1.98 (0.12), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 205 HIS 0.013 0.002 HIS I 32 PHE 0.033 0.002 PHE C 185 TYR 0.023 0.002 TYR B 782 ARG 0.023 0.001 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 420 time to evaluate : 4.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.6078 (OUTLIER) cc_final: 0.4596 (t80) REVERT: A 225 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7689 (p0) REVERT: A 308 GLU cc_start: 0.8237 (pt0) cc_final: 0.7886 (pt0) REVERT: A 351 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7299 (mpt90) REVERT: A 680 MET cc_start: 0.8191 (tpp) cc_final: 0.7788 (ttm) REVERT: A 860 ASP cc_start: 0.8205 (m-30) cc_final: 0.7987 (m-30) REVERT: A 946 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6869 (mm) REVERT: A 1023 MET cc_start: 0.8337 (mmm) cc_final: 0.8128 (mmt) REVERT: B 254 MET cc_start: 0.8327 (mmt) cc_final: 0.7633 (mmt) REVERT: B 272 CYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7424 (m) REVERT: B 527 CYS cc_start: 0.6652 (m) cc_final: 0.6141 (m) REVERT: B 600 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.6619 (ptmm) REVERT: B 634 ASP cc_start: 0.6681 (p0) cc_final: 0.6373 (p0) REVERT: B 635 VAL cc_start: 0.9032 (t) cc_final: 0.8828 (m) REVERT: B 697 ILE cc_start: 0.8888 (tp) cc_final: 0.8580 (mp) REVERT: B 886 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7069 (mtm110) REVERT: K 30 VAL cc_start: 0.6993 (OUTLIER) cc_final: 0.6450 (t) REVERT: L 48 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7698 (ttm-80) REVERT: O 427 ASN cc_start: 0.8219 (t0) cc_final: 0.7736 (t0) REVERT: Q 54 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8073 (tm-30) REVERT: Q 111 MET cc_start: 0.7213 (mmm) cc_final: 0.6810 (tmm) outliers start: 172 outliers final: 102 residues processed: 558 average time/residue: 0.4629 time to fit residues: 428.9141 Evaluate side-chains 492 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 381 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 787 PHE Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 886 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 266 HIS Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 61 ASN Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 395 LEU Chi-restraints excluded: chain O residue 415 HIS Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 375 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 267 optimal weight: 0.5980 chunk 172 optimal weight: 10.0000 chunk 258 optimal weight: 0.2980 chunk 130 optimal weight: 0.0060 chunk 85 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 275 optimal weight: 8.9990 chunk 294 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 340 optimal weight: 9.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 GLN C 59 ASN C 172 HIS C 181 GLN G 23 ASN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN P 240 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN E 132 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN D 85 GLN M 66 ASN M 121 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.8239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37617 Z= 0.199 Angle : 0.753 14.878 50956 Z= 0.364 Chirality : 0.045 0.303 5761 Planarity : 0.005 0.097 6377 Dihedral : 10.830 179.599 5431 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.25 % Favored : 91.55 % Rotamer: Outliers : 2.72 % Allowed : 26.63 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.12), residues: 4437 helix: -0.09 (0.13), residues: 1512 sheet: -2.06 (0.22), residues: 516 loop : -1.88 (0.13), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP M 205 HIS 0.009 0.001 HIS I 32 PHE 0.038 0.001 PHE C 185 TYR 0.017 0.001 TYR B1003 ARG 0.009 0.001 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 455 time to evaluate : 4.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TYR cc_start: 0.8025 (m-80) cc_final: 0.7593 (m-80) REVERT: A 225 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7443 (p0) REVERT: A 308 GLU cc_start: 0.8140 (pt0) cc_final: 0.7549 (pt0) REVERT: A 680 MET cc_start: 0.8050 (tpp) cc_final: 0.7670 (ttm) REVERT: B 254 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7564 (mmt) REVERT: B 272 CYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7471 (m) REVERT: B 364 LEU cc_start: 0.8013 (tt) cc_final: 0.7781 (tp) REVERT: B 525 LEU cc_start: 0.7810 (tp) cc_final: 0.7540 (pt) REVERT: B 527 CYS cc_start: 0.6503 (m) cc_final: 0.5839 (m) REVERT: B 600 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6384 (ptmm) REVERT: B 634 ASP cc_start: 0.6457 (p0) cc_final: 0.6160 (p0) REVERT: B 635 VAL cc_start: 0.8972 (t) cc_final: 0.8771 (m) REVERT: B 697 ILE cc_start: 0.8872 (tp) cc_final: 0.8546 (mp) REVERT: B 1009 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: G 190 ILE cc_start: 0.7364 (mt) cc_final: 0.7058 (mm) REVERT: L 48 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7739 (ttm-80) REVERT: P 196 ARG cc_start: 0.8920 (tpp-160) cc_final: 0.8569 (tpm170) REVERT: P 232 MET cc_start: 0.5720 (mmp) cc_final: 0.5403 (mmp) REVERT: J 6 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7253 (mmt90) REVERT: O 118 MET cc_start: 0.8198 (tmm) cc_final: 0.7608 (tpt) REVERT: O 271 LEU cc_start: 0.7885 (mt) cc_final: 0.7227 (tt) REVERT: O 427 ASN cc_start: 0.8205 (t0) cc_final: 0.7669 (t0) REVERT: Q 54 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8039 (tm-30) outliers start: 108 outliers final: 83 residues processed: 538 average time/residue: 0.5015 time to fit residues: 452.3271 Evaluate side-chains 506 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 416 time to evaluate : 4.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 266 HIS Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 415 HIS Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 375 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 393 optimal weight: 5.9990 chunk 414 optimal weight: 9.9990 chunk 378 optimal weight: 0.3980 chunk 403 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 316 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 364 optimal weight: 4.9990 chunk 381 optimal weight: 20.0000 chunk 401 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 ASN ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.8688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 37617 Z= 0.316 Angle : 0.785 14.811 50956 Z= 0.387 Chirality : 0.045 0.230 5761 Planarity : 0.005 0.091 6377 Dihedral : 10.772 179.572 5431 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.47 % Favored : 90.38 % Rotamer: Outliers : 2.84 % Allowed : 26.66 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.13), residues: 4437 helix: -0.01 (0.13), residues: 1516 sheet: -2.10 (0.22), residues: 518 loop : -1.89 (0.13), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 205 HIS 0.008 0.001 HIS I 32 PHE 0.036 0.002 PHE C 185 TYR 0.021 0.002 TYR E 125 ARG 0.010 0.001 ARG O 533 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 395 time to evaluate : 4.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8468 (mtm) cc_final: 0.8203 (mtm) REVERT: A 140 ARG cc_start: 0.8314 (mtm110) cc_final: 0.7938 (mtm110) REVERT: A 225 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7685 (p0) REVERT: A 308 GLU cc_start: 0.8210 (pt0) cc_final: 0.7781 (pt0) REVERT: A 680 MET cc_start: 0.8128 (tpp) cc_final: 0.7870 (ttm) REVERT: B 186 LYS cc_start: 0.7485 (tmtt) cc_final: 0.7160 (tptt) REVERT: B 254 MET cc_start: 0.8235 (mmt) cc_final: 0.7715 (mmt) REVERT: B 525 LEU cc_start: 0.7743 (tp) cc_final: 0.7511 (pt) REVERT: B 527 CYS cc_start: 0.6879 (m) cc_final: 0.5853 (m) REVERT: B 600 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.6700 (ptmm) REVERT: B 634 ASP cc_start: 0.6720 (p0) cc_final: 0.6377 (p0) REVERT: B 697 ILE cc_start: 0.8866 (tp) cc_final: 0.8585 (mp) REVERT: G 190 ILE cc_start: 0.7596 (mt) cc_final: 0.7223 (mm) REVERT: L 48 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7688 (ttm-80) REVERT: P 232 MET cc_start: 0.5950 (mmp) cc_final: 0.5647 (mmp) REVERT: J 6 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7430 (mmt90) REVERT: O 271 LEU cc_start: 0.8216 (mt) cc_final: 0.7558 (tt) REVERT: O 427 ASN cc_start: 0.8433 (t0) cc_final: 0.7718 (t0) REVERT: Q 54 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8171 (tm-30) REVERT: Q 85 GLU cc_start: 0.6173 (tp30) cc_final: 0.4987 (tm-30) outliers start: 113 outliers final: 87 residues processed: 481 average time/residue: 0.4494 time to fit residues: 361.3255 Evaluate side-chains 471 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 380 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 266 HIS Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 415 HIS Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 375 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 264 optimal weight: 0.9980 chunk 426 optimal weight: 7.9990 chunk 260 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 296 optimal weight: 9.9990 chunk 447 optimal weight: 10.0000 chunk 411 optimal weight: 4.9990 chunk 356 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 275 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1364 HIS ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 829 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 HIS ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.8946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37617 Z= 0.245 Angle : 0.764 14.154 50956 Z= 0.369 Chirality : 0.045 0.274 5761 Planarity : 0.005 0.097 6377 Dihedral : 10.723 178.620 5430 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.68 % Favored : 91.17 % Rotamer: Outliers : 2.44 % Allowed : 27.57 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.13), residues: 4437 helix: 0.07 (0.13), residues: 1520 sheet: -2.07 (0.22), residues: 531 loop : -1.86 (0.13), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP M 205 HIS 0.007 0.001 HIS M 149 PHE 0.036 0.001 PHE C 185 TYR 0.022 0.001 TYR A 83 ARG 0.010 0.000 ARG M 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 396 time to evaluate : 4.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7538 (p0) REVERT: A 308 GLU cc_start: 0.8138 (pt0) cc_final: 0.7779 (pt0) REVERT: A 351 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7145 (mpt90) REVERT: A 680 MET cc_start: 0.8128 (tpp) cc_final: 0.7792 (ttm) REVERT: A 860 ASP cc_start: 0.8126 (m-30) cc_final: 0.7872 (m-30) REVERT: B 186 LYS cc_start: 0.7507 (tmtt) cc_final: 0.7076 (tptt) REVERT: B 525 LEU cc_start: 0.7980 (tp) cc_final: 0.7712 (pt) REVERT: B 600 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.6630 (ptmm) REVERT: B 634 ASP cc_start: 0.6885 (p0) cc_final: 0.6529 (p0) REVERT: B 697 ILE cc_start: 0.8864 (tp) cc_final: 0.8584 (mp) REVERT: G 90 LYS cc_start: 0.8291 (mmtm) cc_final: 0.8047 (mptt) REVERT: G 190 ILE cc_start: 0.7638 (mt) cc_final: 0.7329 (mm) REVERT: L 48 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7650 (ttm-80) REVERT: P 232 MET cc_start: 0.5937 (mmp) cc_final: 0.5636 (mmp) REVERT: P 250 MET cc_start: 0.8974 (mmp) cc_final: 0.8605 (mtm) REVERT: J 6 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7412 (mmt90) REVERT: O 118 MET cc_start: 0.8217 (tmm) cc_final: 0.7634 (tpt) REVERT: O 259 MET cc_start: 0.8341 (ppp) cc_final: 0.7977 (ppp) REVERT: O 271 LEU cc_start: 0.8347 (mt) cc_final: 0.7731 (tt) REVERT: O 427 ASN cc_start: 0.8411 (t0) cc_final: 0.7805 (t0) REVERT: O 434 MET cc_start: 0.8231 (ppp) cc_final: 0.8025 (ppp) REVERT: Q 54 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8138 (tm-30) REVERT: Q 85 GLU cc_start: 0.5915 (tp30) cc_final: 0.5142 (tm-30) outliers start: 97 outliers final: 78 residues processed: 472 average time/residue: 0.4674 time to fit residues: 369.6084 Evaluate side-chains 462 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 379 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 266 HIS Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 415 HIS Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 375 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 282 optimal weight: 10.0000 chunk 379 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 328 optimal weight: 7.9990 chunk 52 optimal weight: 0.0570 chunk 98 optimal weight: 10.0000 chunk 356 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 366 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 overall best weight: 2.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 HIS ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.068117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.054917 restraints weight = 197035.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.056403 restraints weight = 109955.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.057411 restraints weight = 73132.442| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.9257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37617 Z= 0.269 Angle : 0.772 15.306 50956 Z= 0.375 Chirality : 0.045 0.250 5761 Planarity : 0.005 0.092 6377 Dihedral : 10.653 177.752 5428 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.35 % Favored : 90.49 % Rotamer: Outliers : 2.59 % Allowed : 27.54 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.13), residues: 4437 helix: 0.14 (0.13), residues: 1518 sheet: -1.97 (0.22), residues: 518 loop : -1.87 (0.13), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP M 205 HIS 0.007 0.001 HIS M 149 PHE 0.034 0.001 PHE C 185 TYR 0.015 0.001 TYR B 674 ARG 0.011 0.001 ARG A 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9221.33 seconds wall clock time: 166 minutes 40.47 seconds (10000.47 seconds total)