Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 13:38:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn3_30779/05_2023/7dn3_30779_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn3_30779/05_2023/7dn3_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_30779/05_2023/7dn3_30779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn3_30779/05_2023/7dn3_30779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn3_30779/05_2023/7dn3_30779_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn3_30779/05_2023/7dn3_30779_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.049 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 19.22, per 1000 atoms: 0.52 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: 15.14 Conformation dependent library (CDL) restraints added in 5.4 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: 4.64 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: 11.85 Time building geometry restraints manager: 16.32 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: 22126 35.52 - 71.04: 762 71.04 - 106.56: 29 106.56 - 142.08: 0 142.08 - 177.59: 1 Dihedral angle restraints: 22918 sinusoidal: 9775 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 22915 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.440 Check model and map are aligned: 0.570 Set scattering table: 0.330 Process input model: 101.520 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.800 ------------------------------------------------------------------------------- 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 : 16.915 177.595 14414 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 % 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 *********************** 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 : 4.797 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 outliers start: 188 outliers final: 48 residues processed: 1248 average time/residue: 0.5551 time to fit residues: 1080.9410 Evaluate side-chains 637 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 589 time to evaluate : 4.405 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 2 residues processed: 48 average time/residue: 0.4559 time to fit residues: 43.5412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 116 optimal weight: 8.9990 chunk 229 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 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: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN ** A 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A1190 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN 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 642 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 ** 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 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: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 37617 Z= 0.273 Angle : 0.853 16.513 50956 Z= 0.432 Chirality : 0.049 0.256 5761 Planarity : 0.006 0.101 6377 Dihedral : 11.157 179.321 5361 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.34 % Favored : 91.44 % Rotamer Outliers : 4.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.75 (0.11), residues: 4437 helix: -2.31 (0.11), residues: 1542 sheet: -2.73 (0.20), residues: 513 loop : -2.57 (0.12), residues: 2382 *********************** 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 832 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 664 time to evaluate : 4.466 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 outliers start: 168 outliers final: 75 residues processed: 778 average time/residue: 0.5193 time to fit residues: 662.0286 Evaluate side-chains 591 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 516 time to evaluate : 4.994 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.4113 time to fit residues: 62.1641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 226 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 339 optimal weight: 0.0270 chunk 277 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 408 optimal weight: 6.9990 chunk 441 optimal weight: 2.9990 chunk 363 optimal weight: 5.9990 chunk 405 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 327 optimal weight: 0.2980 overall best weight: 1.6644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 94 HIS A 157 HIS A 422 GLN A 693 ASN A 794 GLN A 815 ASN A1039 GLN A1190 GLN ** 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** ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS K 101 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 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 GLN ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 37617 Z= 0.246 Angle : 0.767 15.172 50956 Z= 0.384 Chirality : 0.046 0.306 5761 Planarity : 0.005 0.088 6377 Dihedral : 10.689 176.363 5361 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.63 % Favored : 91.17 % Rotamer Outliers : 2.97 % 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: -3.01 (0.12), residues: 4437 helix: -1.35 (0.12), residues: 1537 sheet: -2.42 (0.20), residues: 525 loop : -2.37 (0.12), residues: 2375 *********************** 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 698 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 580 time to evaluate : 4.589 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 outliers start: 118 outliers final: 44 residues processed: 666 average time/residue: 0.5049 time to fit residues: 552.2881 Evaluate side-chains 540 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 496 time to evaluate : 4.414 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.3730 time to fit residues: 37.4926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 403 optimal weight: 0.8980 chunk 307 optimal weight: 5.9990 chunk 211 optimal weight: 0.0970 chunk 45 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 274 optimal weight: 20.0000 chunk 409 optimal weight: 0.0000 chunk 434 optimal weight: 20.0000 chunk 214 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** 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 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 HIS ** 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 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 HIS ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 HIS N 338 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 37617 Z= 0.211 Angle : 0.730 16.107 50956 Z= 0.359 Chirality : 0.045 0.255 5761 Planarity : 0.005 0.088 6377 Dihedral : 10.451 177.806 5361 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.34 % Favored : 91.44 % Rotamer Outliers : 2.24 % 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: -2.58 (0.12), residues: 4437 helix: -0.89 (0.13), residues: 1538 sheet: -2.21 (0.21), residues: 500 loop : -2.19 (0.12), residues: 2399 *********************** 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 637 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 548 time to evaluate : 4.699 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 outliers start: 89 outliers final: 40 residues processed: 605 average time/residue: 0.5095 time to fit residues: 506.0923 Evaluate side-chains 531 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 491 time to evaluate : 4.721 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3602 time to fit residues: 33.5303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 361 optimal weight: 0.2980 chunk 246 optimal weight: 5.9990 chunk 6 optimal weight: 0.0670 chunk 323 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 370 optimal weight: 0.0970 chunk 300 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 221 optimal weight: 0.7980 chunk 389 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.2518 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 GLN C 48 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** 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** F 72 GLN O 68 HIS ** 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 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN M 134 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.5758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 37617 Z= 0.205 Angle : 0.717 15.047 50956 Z= 0.351 Chirality : 0.044 0.340 5761 Planarity : 0.004 0.091 6377 Dihedral : 10.274 178.009 5361 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.59 % Favored : 91.21 % Rotamer Outliers : 1.89 % 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: -2.27 (0.12), residues: 4437 helix: -0.56 (0.13), residues: 1523 sheet: -2.14 (0.22), residues: 498 loop : -2.03 (0.12), residues: 2416 *********************** 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 607 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 532 time to evaluate : 4.662 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 outliers start: 75 outliers final: 36 residues processed: 584 average time/residue: 0.4942 time to fit residues: 476.0346 Evaluate side-chains 504 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 468 time to evaluate : 4.612 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3610 time to fit residues: 30.1954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 146 optimal weight: 8.9990 chunk 390 optimal weight: 7.9990 chunk 85 optimal weight: 0.0050 chunk 254 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 434 optimal weight: 20.0000 chunk 360 optimal weight: 9.9990 chunk 201 optimal weight: 0.9980 chunk 36 optimal weight: 0.0770 chunk 143 optimal weight: 10.0000 chunk 228 optimal weight: 0.9990 overall best weight: 0.6156 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 GLN B 159 ASN ** B 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** 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** ** O 402 ASN ** 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 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** 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: 0.6729 moved from start: 0.6069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 37617 Z= 0.184 Angle : 0.713 14.939 50956 Z= 0.345 Chirality : 0.044 0.263 5761 Planarity : 0.004 0.091 6377 Dihedral : 10.156 178.912 5361 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.18 % Favored : 91.62 % Rotamer Outliers : 1.36 % 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: -2.09 (0.12), residues: 4437 helix: -0.36 (0.13), residues: 1522 sheet: -2.05 (0.22), residues: 500 loop : -1.95 (0.12), residues: 2415 *********************** 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 567 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 513 time to evaluate : 4.774 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 outliers start: 54 outliers final: 18 residues processed: 551 average time/residue: 0.5057 time to fit residues: 464.2674 Evaluate side-chains 479 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 461 time to evaluate : 4.659 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3582 time to fit residues: 18.7443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 418 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 247 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 365 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 chunk 432 optimal weight: 3.9990 chunk 270 optimal weight: 10.0000 chunk 263 optimal weight: 0.4980 chunk 199 optimal weight: 8.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN ** B 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 HIS ** 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** F 72 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 402 ASN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 37617 Z= 0.239 Angle : 0.741 14.294 50956 Z= 0.361 Chirality : 0.045 0.274 5761 Planarity : 0.004 0.084 6377 Dihedral : 10.081 178.857 5361 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.72 % Favored : 91.10 % Rotamer Outliers : 1.81 % 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: -1.89 (0.12), residues: 4437 helix: -0.15 (0.13), residues: 1513 sheet: -1.97 (0.22), residues: 511 loop : -1.84 (0.13), residues: 2413 *********************** 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 549 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 477 time to evaluate : 4.866 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 outliers start: 72 outliers final: 29 residues processed: 521 average time/residue: 0.4889 time to fit residues: 426.5851 Evaluate side-chains 472 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 443 time to evaluate : 5.030 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3467 time to fit residues: 25.5519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 267 optimal weight: 0.0570 chunk 172 optimal weight: 3.9990 chunk 258 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 275 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 213 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 340 optimal weight: 9.9990 overall best weight: 1.4902 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN B 679 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 HIS ** 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** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 507 ASN ** D 41 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 37617 Z= 0.207 Angle : 0.732 15.675 50956 Z= 0.352 Chirality : 0.044 0.276 5761 Planarity : 0.004 0.092 6377 Dihedral : 10.017 179.858 5361 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.34 % Favored : 91.48 % Rotamer Outliers : 0.83 % 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: -1.78 (0.13), residues: 4437 helix: -0.03 (0.14), residues: 1518 sheet: -1.88 (0.22), residues: 509 loop : -1.81 (0.13), residues: 2410 *********************** 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 507 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 474 time to evaluate : 4.643 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 outliers start: 33 outliers final: 15 residues processed: 497 average time/residue: 0.5091 time to fit residues: 423.5643 Evaluate side-chains 455 residues out of total 3993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 440 time to evaluate : 5.357 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3675 time to fit residues: 16.7617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 393 optimal weight: 2.9990 chunk 414 optimal weight: 5.9990 chunk 378 optimal weight: 2.9990 chunk 403 optimal weight: 0.5980 chunk 242 optimal weight: 0.0040 chunk 175 optimal weight: 7.9990 chunk 316 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 364 optimal weight: 8.9990 chunk 381 optimal weight: 0.0770 chunk 401 optimal weight: 4.9990 overall best weight: 1.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: