Starting phenix.real_space_refine (version: dev) on Tue Dec 20 09:28:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gys_0096/12_2022/6gys_0096_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gys_0096/12_2022/6gys_0096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gys_0096/12_2022/6gys_0096.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gys_0096/12_2022/6gys_0096.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gys_0096/12_2022/6gys_0096_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gys_0096/12_2022/6gys_0096_neut.pdb" } resolution = 4.4 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= 0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 17": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "B ARG 4": "NH1" <-> "NH2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C ARG 26": "NH1" <-> "NH2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 17": "NH1" <-> "NH2" Residue "H ARG 95": "NH1" <-> "NH2" Residue "H ARG 128": "NH1" <-> "NH2" Residue "H ARG 308": "NH1" <-> "NH2" Residue "H ARG 313": "NH1" <-> "NH2" Residue "H ARG 322": "NH1" <-> "NH2" Residue "H ARG 330": "NH1" <-> "NH2" Residue "H PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 409": "NH1" <-> "NH2" Residue "H ARG 463": "NH1" <-> "NH2" Residue "H ARG 468": "NH1" <-> "NH2" Residue "I ARG 4": "NH1" <-> "NH2" Residue "I ARG 26": "NH1" <-> "NH2" Residue "I TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 375": "NH1" <-> "NH2" Residue "I ARG 392": "NH1" <-> "NH2" Residue "I ARG 397": "NH1" <-> "NH2" Residue "I ARG 591": "NH1" <-> "NH2" Residue "J ARG 20": "NH1" <-> "NH2" Residue "J ASP 25": "OD1" <-> "OD2" Residue "J ARG 36": "NH1" <-> "NH2" Residue "J ASP 39": "OD1" <-> "OD2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 15": "NH1" <-> "NH2" Residue "K ARG 25": "NH1" <-> "NH2" Residue "K ARG 83": "NH1" <-> "NH2" Residue "K ARG 98": "NH1" <-> "NH2" Residue "K ARG 121": "NH1" <-> "NH2" Residue "K ARG 159": "NH1" <-> "NH2" Residue "K ARG 161": "NH1" <-> "NH2" Residue "K ARG 168": "NH1" <-> "NH2" Residue "K ARG 185": "NH1" <-> "NH2" Residue "K ARG 186": "NH1" <-> "NH2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 38890 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3517 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 409} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 4775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4775 Classifications: {'peptide': 579} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 559} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 4691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4691 Classifications: {'peptide': 573} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 553} Chain breaks: 3 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1226 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 4224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4224 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 471} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1079 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "G" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1053 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "H" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3517 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 409} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 4775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4775 Classifications: {'peptide': 579} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 559} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4575 Classifications: {'peptide': 554} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 534} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1226 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 4224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4224 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 471} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3627 SG CYS B 14 203.383 54.661 134.869 1.00342.11 S ATOM 3646 SG CYS B 17 204.184 58.016 135.776 1.00356.26 S ATOM 3627 SG CYS B 14 203.383 54.661 134.869 1.00342.11 S ATOM 3772 SG CYS B 33 206.706 55.422 136.612 1.00348.22 S ATOM 3845 SG CYS B 42 206.064 52.122 135.186 1.00344.46 S ATOM 8382 SG CYS C 17 157.661 80.210 89.051 1.00413.84 S ATOM 8490 SG CYS C 30 159.575 78.373 85.270 1.00423.48 S ATOM 8363 SG CYS C 14 158.549 81.882 85.933 1.00422.58 S ATOM 8508 SG CYS C 33 156.440 79.722 83.166 1.00425.94 S ATOM 24211 SG CYS I 17 30.422 74.934 88.138 1.00485.92 S ATOM 24319 SG CYS I 30 28.898 75.374 84.976 1.00478.10 S ATOM 24337 SG CYS I 33 26.603 74.544 87.654 1.00502.51 S ATOM 24410 SG CYS I 42 28.353 78.053 87.310 1.00487.62 S ATOM 28899 SG CYS J 17 94.739 41.790 66.592 1.00742.31 S ATOM 29007 SG CYS J 30 94.178 45.346 66.397 1.00742.87 S ATOM 29007 SG CYS J 30 94.178 45.346 66.397 1.00742.87 S ATOM 29098 SG CYS J 42 96.956 46.476 64.436 1.00749.59 S Time building chain proxies: 21.31, per 1000 atoms: 0.55 Number of scatterers: 38890 At special positions: 0 Unit cell: (258.64, 144.16, 168.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 168 16.00 P 104 15.00 O 7363 8.00 N 6478 7.00 C 24769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 215 " distance=2.04 Simple disulfide: pdb=" SG CYS I 99 " - pdb=" SG CYS I 215 " distance=2.03 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: 17.15 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 17 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 14 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 33 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 42 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 14 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 17 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 30 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 33 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 14 " pdb=" ZN I 701 " pdb="ZN ZN I 701 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 701 " - pdb=" SG CYS I 30 " pdb=" ZN I 702 " pdb="ZN ZN I 702 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 702 " - pdb=" SG CYS I 33 " pdb=" ZN J 701 " pdb="ZN ZN J 701 " - pdb=" SG CYS J 30 " pdb="ZN ZN J 701 " - pdb=" SG CYS J 17 " pdb=" ZN J 702 " pdb="ZN ZN J 702 " - pdb=" SG CYS J 42 " pdb="ZN ZN J 702 " - pdb=" SG CYS J 30 " 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8642 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 14 sheets defined 60.5% alpha, 2.0% beta 47 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 10.84 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.535A pdb=" N PHE A 9 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.645A pdb=" N GLU A 19 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 66 through 71 removed outlier: 3.677A pdb=" N PHE A 70 " --> pdb=" O MET A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.995A pdb=" N GLU A 78 " --> pdb=" O ASN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.895A pdb=" N TYR A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.536A pdb=" N TRP A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 302 through 309 removed outlier: 4.097A pdb=" N ILE A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.856A pdb=" N ASN A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.973A pdb=" N SER A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 435 " --> pdb=" O TRP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 460 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 38 through 44 removed outlier: 3.716A pdb=" N CYS B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 74 removed outlier: 3.845A pdb=" N ASN B 74 " --> pdb=" O TYR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 106 removed outlier: 3.832A pdb=" N PHE B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 125 through 130 removed outlier: 4.133A pdb=" N SER B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 153 through 174 Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.541A pdb=" N HIS B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 202 Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.651A pdb=" N GLN B 222 " --> pdb=" O PHE B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.761A pdb=" N VAL B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 249 through 266 Processing helix chain 'B' and resid 279 through 303 removed outlier: 3.544A pdb=" N GLY B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 357 removed outlier: 3.614A pdb=" N ILE B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.759A pdb=" N LEU B 370 " --> pdb=" O PRO B 366 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 382 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 422 removed outlier: 3.632A pdb=" N ALA B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 446 Processing helix chain 'B' and resid 451 through 455 Processing helix chain 'B' and resid 456 through 477 removed outlier: 3.678A pdb=" N MET B 460 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 495 Processing helix chain 'B' and resid 501 through 524 removed outlier: 3.780A pdb=" N LEU B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 553 removed outlier: 3.668A pdb=" N ASN B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS B 546 " --> pdb=" O GLN B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 589 through 601 removed outlier: 3.850A pdb=" N ILE B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.560A pdb=" N ASP B 605 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE B 606 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 607 " --> pdb=" O SER B 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 602 through 607' Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 32 through 37 removed outlier: 4.155A pdb=" N ARG C 36 " --> pdb=" O ASN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 56 through 70 removed outlier: 3.870A pdb=" N ASP C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 106 Processing helix chain 'C' and resid 107 through 122 removed outlier: 3.729A pdb=" N LEU C 114 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 128 removed outlier: 3.857A pdb=" N TYR C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 149 removed outlier: 3.573A pdb=" N LEU C 136 " --> pdb=" O ASP C 132 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP C 144 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C 148 " --> pdb=" O TRP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 174 removed outlier: 3.560A pdb=" N TYR C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR C 173 " --> pdb=" O MET C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 184 through 192 removed outlier: 4.043A pdb=" N LEU C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 224 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 244 through 249 Processing helix chain 'C' and resid 249 through 265 Processing helix chain 'C' and resid 279 through 303 Processing helix chain 'C' and resid 319 through 327 removed outlier: 5.001A pdb=" N TYR C 325 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 326 " --> pdb=" O HIS C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 356 removed outlier: 3.534A pdb=" N TRP C 346 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 387 removed outlier: 4.526A pdb=" N ILE C 379 " --> pdb=" O ARG C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 423 removed outlier: 3.599A pdb=" N ILE C 402 " --> pdb=" O PHE C 398 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR C 422 " --> pdb=" O TYR C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 445 Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 456 through 477 removed outlier: 4.146A pdb=" N MET C 460 " --> pdb=" O HIS C 456 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR C 464 " --> pdb=" O MET C 460 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 495 removed outlier: 4.044A pdb=" N ALA C 494 " --> pdb=" O THR C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 524 removed outlier: 3.683A pdb=" N SER C 515 " --> pdb=" O THR C 511 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 523 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 553 removed outlier: 3.702A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 548 " --> pdb=" O ASP C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 563 removed outlier: 3.537A pdb=" N GLY C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 601 removed outlier: 4.357A pdb=" N VAL C 594 " --> pdb=" O PHE C 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 25 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 83 through 98 Processing helix chain 'D' and resid 117 through 124 Processing helix chain 'D' and resid 127 through 142 Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.813A pdb=" N VAL D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 169 Processing helix chain 'D' and resid 177 through 189 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 38 through 59 Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.858A pdb=" N LYS E 102 " --> pdb=" O PRO E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 139 removed outlier: 3.584A pdb=" N GLU E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER E 116 " --> pdb=" O GLU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 168 removed outlier: 3.710A pdb=" N LEU E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 192 removed outlier: 3.796A pdb=" N VAL E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 224 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 235 through 239 removed outlier: 3.742A pdb=" N SER E 238 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 334 through 349 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 371 through 378 removed outlier: 3.762A pdb=" N PHE E 378 " --> pdb=" O PHE E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 384 Processing helix chain 'E' and resid 400 through 406 Processing helix chain 'E' and resid 418 through 422 removed outlier: 4.306A pdb=" N LYS E 421 " --> pdb=" O THR E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'E' and resid 436 through 443 removed outlier: 4.333A pdb=" N ASP E 440 " --> pdb=" O PHE E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 479 Proline residue: E 473 - end of helix Processing helix chain 'E' and resid 482 through 486 Processing helix chain 'E' and resid 492 through 503 Processing helix chain 'E' and resid 520 through 525 Processing helix chain 'E' and resid 526 through 534 removed outlier: 3.961A pdb=" N LEU E 534 " --> pdb=" O PHE E 530 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 12 removed outlier: 3.546A pdb=" N PHE H 9 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU H 12 " --> pdb=" O ARG H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 24 removed outlier: 3.836A pdb=" N GLU H 19 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL H 20 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR H 21 " --> pdb=" O ARG H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 66 Processing helix chain 'H' and resid 67 through 70 Processing helix chain 'H' and resid 73 through 78 removed outlier: 4.019A pdb=" N GLU H 78 " --> pdb=" O ASN H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 94 removed outlier: 3.586A pdb=" N ILE H 84 " --> pdb=" O SER H 80 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU H 88 " --> pdb=" O ILE H 84 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLU H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR H 90 " --> pdb=" O LYS H 86 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP H 93 " --> pdb=" O GLU H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 111 Processing helix chain 'H' and resid 143 through 151 removed outlier: 3.865A pdb=" N VAL H 151 " --> pdb=" O TYR H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 164 Processing helix chain 'H' and resid 176 through 190 removed outlier: 4.003A pdb=" N LYS H 190 " --> pdb=" O ILE H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 268 removed outlier: 3.593A pdb=" N SER H 266 " --> pdb=" O ARG H 262 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU H 268 " --> pdb=" O ILE H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 271 No H-bonds generated for 'chain 'H' and resid 269 through 271' Processing helix chain 'H' and resid 280 through 288 Processing helix chain 'H' and resid 302 through 309 removed outlier: 3.626A pdb=" N ILE H 309 " --> pdb=" O VAL H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 350 removed outlier: 3.679A pdb=" N SER H 349 " --> pdb=" O ASP H 346 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE H 350 " --> pdb=" O LEU H 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 346 through 350' Processing helix chain 'H' and resid 371 through 380 removed outlier: 4.123A pdb=" N ASN H 375 " --> pdb=" O ASN H 371 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS H 378 " --> pdb=" O GLU H 374 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU H 379 " --> pdb=" O ASN H 375 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU H 380 " --> pdb=" O ILE H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 389 Processing helix chain 'H' and resid 423 through 433 removed outlier: 3.615A pdb=" N SER H 433 " --> pdb=" O ILE H 429 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 460 Processing helix chain 'H' and resid 461 through 463 No H-bonds generated for 'chain 'H' and resid 461 through 463' Processing helix chain 'I' and resid 14 through 21 removed outlier: 3.518A pdb=" N THR I 18 " --> pdb=" O CYS I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 36 removed outlier: 3.613A pdb=" N ARG I 34 " --> pdb=" O CYS I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 44 Processing helix chain 'I' and resid 56 through 72 removed outlier: 4.648A pdb=" N ASP I 60 " --> pdb=" O GLU I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 79 removed outlier: 3.577A pdb=" N TYR I 78 " --> pdb=" O ASN I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 106 removed outlier: 3.547A pdb=" N TRP I 102 " --> pdb=" O GLU I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 122 removed outlier: 3.995A pdb=" N LEU I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU I 120 " --> pdb=" O ASN I 116 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN I 121 " --> pdb=" O PHE I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 130 Processing helix chain 'I' and resid 133 through 144 Processing helix chain 'I' and resid 153 through 174 removed outlier: 3.524A pdb=" N ILE I 163 " --> pdb=" O TRP I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 183 Processing helix chain 'I' and resid 185 through 193 removed outlier: 4.258A pdb=" N HIS I 189 " --> pdb=" O VAL I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 202 Processing helix chain 'I' and resid 203 through 224 removed outlier: 3.821A pdb=" N VAL I 207 " --> pdb=" O GLY I 203 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN I 219 " --> pdb=" O CYS I 215 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN I 222 " --> pdb=" O PHE I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 242 removed outlier: 4.124A pdb=" N VAL I 234 " --> pdb=" O ASP I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 244 through 249 Processing helix chain 'I' and resid 249 through 268 removed outlier: 4.035A pdb=" N ALA I 253 " --> pdb=" O GLU I 249 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE I 267 " --> pdb=" O THR I 263 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS I 268 " --> pdb=" O PHE I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 303 removed outlier: 3.884A pdb=" N ARG I 291 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN I 303 " --> pdb=" O CYS I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 356 removed outlier: 3.568A pdb=" N ILE I 349 " --> pdb=" O TYR I 345 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP I 352 " --> pdb=" O ILE I 348 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU I 355 " --> pdb=" O LEU I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 382 removed outlier: 4.155A pdb=" N ASP I 378 " --> pdb=" O ARG I 374 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE I 379 " --> pdb=" O ARG I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 393 through 422 removed outlier: 3.687A pdb=" N ARG I 397 " --> pdb=" O SER I 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 426 through 445 Processing helix chain 'I' and resid 450 through 454 Processing helix chain 'I' and resid 456 through 477 removed outlier: 3.942A pdb=" N MET I 460 " --> pdb=" O HIS I 456 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER I 471 " --> pdb=" O VAL I 467 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE I 476 " --> pdb=" O PHE I 472 " (cutoff:3.500A) Processing helix chain 'I' and resid 479 through 495 removed outlier: 3.638A pdb=" N ASP I 488 " --> pdb=" O GLN I 484 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA I 494 " --> pdb=" O THR I 490 " (cutoff:3.500A) Processing helix chain 'I' and resid 501 through 524 Processing helix chain 'I' and resid 535 through 553 removed outlier: 3.738A pdb=" N LEU I 541 " --> pdb=" O VAL I 537 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE I 545 " --> pdb=" O LEU I 541 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS I 546 " --> pdb=" O GLN I 542 " (cutoff:3.500A) Processing helix chain 'I' and resid 555 through 560 removed outlier: 4.098A pdb=" N LYS I 560 " --> pdb=" O PHE I 556 " (cutoff:3.500A) Processing helix chain 'I' and resid 589 through 593 Processing helix chain 'I' and resid 593 through 601 removed outlier: 4.582A pdb=" N SER I 599 " --> pdb=" O GLU I 595 " (cutoff:3.500A) Processing helix chain 'I' and resid 602 through 607 removed outlier: 3.956A pdb=" N ASP I 605 " --> pdb=" O ASN I 602 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU I 607 " --> pdb=" O SER I 604 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 20 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 62 through 72 removed outlier: 3.908A pdb=" N GLN J 66 " --> pdb=" O LEU J 62 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 106 removed outlier: 4.009A pdb=" N TRP J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU J 106 " --> pdb=" O TRP J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 122 removed outlier: 4.754A pdb=" N LEU J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 130 removed outlier: 3.913A pdb=" N TYR J 126 " --> pdb=" O LEU J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 144 removed outlier: 3.542A pdb=" N LEU J 136 " --> pdb=" O ASP J 132 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP J 144 " --> pdb=" O VAL J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 173 removed outlier: 3.533A pdb=" N VAL J 166 " --> pdb=" O LEU J 162 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE J 171 " --> pdb=" O PHE J 167 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR J 172 " --> pdb=" O THR J 168 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR J 173 " --> pdb=" O MET J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 183 removed outlier: 3.864A pdb=" N GLU J 181 " --> pdb=" O GLU J 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 193 removed outlier: 3.944A pdb=" N LEU J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 224 Processing helix chain 'J' and resid 230 through 241 removed outlier: 4.163A pdb=" N VAL J 234 " --> pdb=" O ASP J 230 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE J 239 " --> pdb=" O GLN J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 249 Processing helix chain 'J' and resid 249 through 267 Processing helix chain 'J' and resid 279 through 303 removed outlier: 3.984A pdb=" N VAL J 287 " --> pdb=" O SER J 283 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE J 292 " --> pdb=" O THR J 288 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN J 303 " --> pdb=" O CYS J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 354 removed outlier: 3.732A pdb=" N TRP J 346 " --> pdb=" O GLU J 342 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE J 348 " --> pdb=" O LEU J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 366 through 383 removed outlier: 4.617A pdb=" N TYR J 382 " --> pdb=" O ASP J 378 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS J 383 " --> pdb=" O ILE J 379 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 420 removed outlier: 4.413A pdb=" N ALA J 403 " --> pdb=" O GLN J 399 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER J 408 " --> pdb=" O LEU J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 427 through 444 removed outlier: 3.580A pdb=" N ASN J 444 " --> pdb=" O SER J 440 " (cutoff:3.500A) Processing helix chain 'J' and resid 450 through 455 Processing helix chain 'J' and resid 456 through 477 removed outlier: 3.584A pdb=" N THR J 464 " --> pdb=" O MET J 460 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER J 471 " --> pdb=" O VAL J 467 " (cutoff:3.500A) Processing helix chain 'J' and resid 479 through 496 removed outlier: 3.567A pdb=" N LYS J 483 " --> pdb=" O SER J 479 " (cutoff:3.500A) Processing helix chain 'J' and resid 497 through 500 removed outlier: 4.169A pdb=" N PHE J 500 " --> pdb=" O PRO J 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 497 through 500' Processing helix chain 'J' and resid 501 through 524 removed outlier: 3.730A pdb=" N ASP J 505 " --> pdb=" O GLY J 501 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS J 506 " --> pdb=" O SER J 502 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU J 507 " --> pdb=" O LYS J 503 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU J 514 " --> pdb=" O LEU J 510 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER J 515 " --> pdb=" O THR J 511 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL J 524 " --> pdb=" O LEU J 520 " (cutoff:3.500A) Processing helix chain 'J' and resid 535 through 552 removed outlier: 3.819A pdb=" N ILE J 545 " --> pdb=" O LEU J 541 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE J 548 " --> pdb=" O ASP J 544 " (cutoff:3.500A) Processing helix chain 'J' and resid 554 through 562 Processing helix chain 'J' and resid 592 through 601 Processing helix chain 'J' and resid 602 through 607 removed outlier: 3.878A pdb=" N ILE J 606 " --> pdb=" O ILE J 603 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 24 Processing helix chain 'K' and resid 26 through 33 Processing helix chain 'K' and resid 83 through 97 Processing helix chain 'K' and resid 117 through 124 Processing helix chain 'K' and resid 127 through 141 Processing helix chain 'K' and resid 143 through 159 Processing helix chain 'K' and resid 162 through 169 Processing helix chain 'K' and resid 177 through 188 Processing helix chain 'L' and resid 29 through 35 Processing helix chain 'L' and resid 38 through 59 removed outlier: 3.803A pdb=" N THR L 50 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 93 Processing helix chain 'L' and resid 109 through 139 removed outlier: 3.734A pdb=" N VAL L 138 " --> pdb=" O LYS L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 169 removed outlier: 3.917A pdb=" N LEU L 151 " --> pdb=" O ASP L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 191 Processing helix chain 'L' and resid 207 through 224 Processing helix chain 'L' and resid 227 through 232 Processing helix chain 'L' and resid 281 through 295 Processing helix chain 'L' and resid 334 through 349 removed outlier: 3.567A pdb=" N PHE L 338 " --> pdb=" O ARG L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 359 Processing helix chain 'L' and resid 400 through 408 Processing helix chain 'L' and resid 418 through 422 removed outlier: 3.800A pdb=" N LYS L 421 " --> pdb=" O THR L 418 " (cutoff:3.500A) Processing helix chain 'L' and resid 428 through 435 removed outlier: 3.587A pdb=" N ILE L 435 " --> pdb=" O LEU L 431 " (cutoff:3.500A) Processing helix chain 'L' and resid 437 through 445 removed outlier: 3.565A pdb=" N GLU L 441 " --> pdb=" O PRO L 437 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 479 removed outlier: 3.523A pdb=" N ARG L 455 " --> pdb=" O SER L 451 " (cutoff:3.500A) Proline residue: L 473 - end of helix Processing helix chain 'L' and resid 487 through 491 Processing helix chain 'L' and resid 492 through 503 Processing helix chain 'L' and resid 504 through 509 removed outlier: 4.635A pdb=" N LYS L 507 " --> pdb=" O ILE L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 526 through 534 removed outlier: 3.741A pdb=" N LEU L 534 " --> pdb=" O PHE L 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 140 removed outlier: 7.120A pdb=" N TYR A 131 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 118 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ILE A 168 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 276 through 278 removed outlier: 6.622A pdb=" N ILE A 276 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 337 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 344 through 345 Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 411 removed outlier: 5.784A pdb=" N ILE A 452 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 478 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 454 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'D' and resid 15 through 19 removed outlier: 3.845A pdb=" N ILE D 75 " --> pdb=" O ASN D 5 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET D 77 " --> pdb=" O VAL D 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 253 through 254 Processing sheet with id=AA8, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.630A pdb=" N VAL L 73 " --> pdb=" O VAL H 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 118 through 120 removed outlier: 4.297A pdb=" N VAL H 140 " --> pdb=" O TYR H 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 276 through 278 removed outlier: 6.352A pdb=" N ILE H 276 " --> pdb=" O ARG H 313 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N SER H 315 " --> pdb=" O ILE H 276 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N VAL H 278 " --> pdb=" O SER H 315 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N MET H 317 " --> pdb=" O VAL H 278 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE H 312 " --> pdb=" O VAL H 338 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER H 340 " --> pdb=" O ILE H 312 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU H 314 " --> pdb=" O SER H 340 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL H 342 " --> pdb=" O LEU H 314 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ARG H 316 " --> pdb=" O VAL H 342 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU H 337 " --> pdb=" O SER H 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 344 through 345 Processing sheet with id=AB3, first strand: chain 'H' and resid 410 through 411 removed outlier: 5.557A pdb=" N ILE H 452 " --> pdb=" O LEU H 476 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 16 through 19 removed outlier: 7.821A pdb=" N VAL K 79 " --> pdb=" O VAL K 7 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL K 9 " --> pdb=" O VAL K 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 240 through 241 1682 hydrogen bonds defined for protein. 4914 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 12.65 Time building geometry restraints manager: 18.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9666 1.33 - 1.45: 10131 1.45 - 1.58: 19766 1.58 - 1.70: 207 1.70 - 1.83: 250 Bond restraints: 40020 Sorted by residual: bond pdb=" C LYS B 308 " pdb=" N PRO B 309 " ideal model delta sigma weight residual 1.336 1.288 0.048 9.80e-03 1.04e+04 2.40e+01 bond pdb=" C LEU L 37 " pdb=" N LYS L 38 " ideal model delta sigma weight residual 1.330 1.265 0.065 1.47e-02 4.63e+03 1.95e+01 bond pdb=" C TYR J 186 " pdb=" N PRO J 187 " ideal model delta sigma weight residual 1.337 1.385 -0.049 1.11e-02 8.12e+03 1.91e+01 bond pdb=" C PRO H 33 " pdb=" N TYR H 34 " ideal model delta sigma weight residual 1.331 1.242 0.089 2.07e-02 2.33e+03 1.85e+01 bond pdb=" C LEU C 58 " pdb=" N PRO C 59 " ideal model delta sigma weight residual 1.336 1.387 -0.051 1.20e-02 6.94e+03 1.82e+01 ... (remaining 40015 not shown) Histogram of bond angle deviations from ideal: 94.72 - 102.90: 375 102.90 - 111.08: 15419 111.08 - 119.26: 18045 119.26 - 127.44: 20226 127.44 - 135.62: 545 Bond angle restraints: 54610 Sorted by residual: angle pdb=" C LEU A 286 " pdb=" N LEU A 287 " pdb=" CA LEU A 287 " ideal model delta sigma weight residual 122.36 109.17 13.19 1.72e+00 3.38e-01 5.88e+01 angle pdb=" C LEU H 286 " pdb=" N LEU H 287 " pdb=" CA LEU H 287 " ideal model delta sigma weight residual 122.36 109.92 12.44 1.72e+00 3.38e-01 5.23e+01 angle pdb=" N LYS E 260 " pdb=" CA LYS E 260 " pdb=" C LYS E 260 " ideal model delta sigma weight residual 114.09 103.28 10.81 1.55e+00 4.16e-01 4.87e+01 angle pdb=" C LYS A 368 " pdb=" N TRP A 369 " pdb=" CA TRP A 369 " ideal model delta sigma weight residual 121.54 133.17 -11.63 1.91e+00 2.74e-01 3.71e+01 angle pdb=" CA LEU H 24 " pdb=" CB LEU H 24 " pdb=" CG LEU H 24 " ideal model delta sigma weight residual 116.30 135.62 -19.32 3.50e+00 8.16e-02 3.05e+01 ... (remaining 54605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 22955 34.44 - 68.89: 708 68.89 - 103.33: 52 103.33 - 137.77: 0 137.77 - 172.22: 1 Dihedral angle restraints: 23716 sinusoidal: 10449 harmonic: 13267 Sorted by residual: dihedral pdb=" CA THR L 263 " pdb=" C THR L 263 " pdb=" N PRO L 264 " pdb=" CA PRO L 264 " ideal model delta harmonic sigma weight residual -180.00 -142.92 -37.08 0 5.00e+00 4.00e-02 5.50e+01 dihedral pdb=" CA ASP A 116 " pdb=" C ASP A 116 " pdb=" N ALA A 117 " pdb=" CA ALA A 117 " ideal model delta harmonic sigma weight residual 180.00 143.18 36.82 0 5.00e+00 4.00e-02 5.42e+01 dihedral pdb=" CA ARG H 274 " pdb=" C ARG H 274 " pdb=" N LYS H 275 " pdb=" CA LYS H 275 " ideal model delta harmonic sigma weight residual 180.00 143.35 36.65 0 5.00e+00 4.00e-02 5.37e+01 ... (remaining 23713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 5520 0.098 - 0.196: 471 0.196 - 0.294: 26 0.294 - 0.392: 2 0.392 - 0.490: 1 Chirality restraints: 6020 Sorted by residual: chirality pdb=" CB ILE H 301 " pdb=" CA ILE H 301 " pdb=" CG1 ILE H 301 " pdb=" CG2 ILE H 301 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" C1' DA G 35 " pdb=" O4' DA G 35 " pdb=" C2' DA G 35 " pdb=" N9 DA G 35 " both_signs ideal model delta sigma weight residual False 2.42 2.12 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE A 301 " pdb=" CA ILE A 301 " pdb=" CG1 ILE A 301 " pdb=" CG2 ILE A 301 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 6017 not shown) Planarity restraints: 6548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE H 328 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C PHE H 328 " 0.065 2.00e-02 2.50e+03 pdb=" O PHE H 328 " -0.025 2.00e-02 2.50e+03 pdb=" N THR H 329 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 328 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C PHE A 328 " 0.056 2.00e-02 2.50e+03 pdb=" O PHE A 328 " -0.021 2.00e-02 2.50e+03 pdb=" N THR A 329 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 443 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C GLN H 443 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN H 443 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN H 444 " 0.018 2.00e-02 2.50e+03 ... (remaining 6545 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.68: 2 1.68 - 2.48: 431 2.48 - 3.29: 46948 3.29 - 4.09: 106265 4.09 - 4.90: 184481 Warning: very small nonbonded interaction distances. Nonbonded interactions: 338127 Sorted by model distance: nonbonded pdb=" CD1 ILE I 28 " pdb=" CG2 ILE I 49 " model vdw 0.873 3.880 nonbonded pdb=" CG1 ILE I 28 " pdb=" CG2 ILE I 49 " model vdw 1.306 3.860 nonbonded pdb=" OP2 DA F 34 " pdb=" NH1 ARG L 334 " model vdw 1.808 2.520 nonbonded pdb=" OD2 ASP A 97 " pdb=" NH2 ARG D 161 " model vdw 1.864 2.520 nonbonded pdb=" CD1 ILE I 28 " pdb=" CB ILE I 49 " model vdw 1.865 3.890 ... (remaining 338122 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' } ncs_group { reference = (chain 'B' and (resid 12 through 46 or resid 49 through 315 or resid 339 or (res \ id 340 and (name N or name CA or name C or name O or name CB )) or resid 341 thr \ ough 608 or resid 701 through 702)) selection = (chain 'C' and (resid 12 through 315 or resid 339 through 608 or resid 701 throu \ gh 702)) selection = (chain 'I' and (resid 12 through 46 or resid 49 through 315 or resid 339 or (res \ id 340 and (name N or name CA or name C or name O or name CB )) or resid 341 thr \ ough 608 or resid 701 through 702)) selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 104 5.49 5 S 168 5.16 5 C 24769 2.51 5 N 6478 2.21 5 O 7363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 15.920 Check model and map are aligned: 0.620 Convert atoms to be neutral: 0.350 Process input model: 111.300 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.008 0.105 40020 Z= 0.509 Angle : 1.122 19.322 54610 Z= 0.643 Chirality : 0.058 0.490 6020 Planarity : 0.007 0.076 6548 Dihedral : 15.133 172.218 15068 Min Nonbonded Distance : 0.873 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.81 % Favored : 89.10 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.10), residues: 4385 helix: -2.34 (0.08), residues: 2435 sheet: -3.92 (0.33), residues: 170 loop : -3.07 (0.13), residues: 1780 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 403 time to evaluate : 4.521 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 outliers start: 23 outliers final: 3 residues processed: 424 average time/residue: 0.5611 time to fit residues: 375.3602 Evaluate side-chains 209 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 206 time to evaluate : 4.792 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.3357 time to fit residues: 8.5145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 379 optimal weight: 8.9990 chunk 341 optimal weight: 8.9990 chunk 189 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 182 optimal weight: 0.9980 chunk 352 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 214 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 chunk 408 optimal weight: 2.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 439 HIS ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN B 66 GLN B 152 HIS ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 445 ASN B 543 ASN C 66 GLN C 211 ASN C 259 GLN C 445 ASN C 461 GLN C 495 ASN C 552 ASN C 598 GLN D 128 GLN D 174 ASN E 57 GLN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 HIS ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN H 296 ASN H 348 ASN H 420 GLN ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 450 ASN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN I 104 ASN I 152 HIS I 228 HIS I 254 ASN I 461 GLN I 495 ASN I 543 ASN J 116 ASN ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN L 86 HIS L 268 GLN ** L 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 40020 Z= 0.248 Angle : 0.743 14.351 54610 Z= 0.400 Chirality : 0.044 0.288 6020 Planarity : 0.006 0.202 6548 Dihedral : 17.694 166.677 5889 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.30 % Favored : 90.63 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.94 (0.11), residues: 4385 helix: -1.26 (0.09), residues: 2547 sheet: -3.27 (0.41), residues: 136 loop : -2.81 (0.14), residues: 1702 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 308 time to evaluate : 4.783 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: 6 outliers final: 1 residues processed: 312 average time/residue: 0.5627 time to fit residues: 280.5924 Evaluate side-chains 205 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 5.030 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3686 time to fit residues: 7.3886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 227 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 340 optimal weight: 8.9990 chunk 278 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 409 optimal weight: 0.9980 chunk 442 optimal weight: 7.9990 chunk 364 optimal weight: 5.9990 chunk 405 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 328 optimal weight: 50.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN A 443 GLN B 406 GLN B 569 ASN C 303 GLN D 31 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS E 340 ASN ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN H 348 ASN ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 444 ASN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 254 ASN ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 543 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN L 471 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 40020 Z= 0.242 Angle : 0.701 14.194 54610 Z= 0.375 Chirality : 0.043 0.242 6020 Planarity : 0.005 0.090 6548 Dihedral : 17.453 167.434 5889 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.49 % Favored : 90.44 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.12), residues: 4385 helix: -0.79 (0.09), residues: 2544 sheet: -3.03 (0.46), residues: 106 loop : -2.62 (0.14), residues: 1735 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 259 time to evaluate : 4.793 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 outliers start: 5 outliers final: 1 residues processed: 264 average time/residue: 0.5346 time to fit residues: 232.4467 Evaluate side-chains 194 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 4.551 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3364 time to fit residues: 6.7546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 404 optimal weight: 0.9990 chunk 307 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 chunk 274 optimal weight: 20.0000 chunk 410 optimal weight: 2.9990 chunk 434 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 389 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN C 303 GLN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 474 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 447 HIS ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 40020 Z= 0.256 Angle : 0.698 13.745 54610 Z= 0.373 Chirality : 0.043 0.268 6020 Planarity : 0.005 0.103 6548 Dihedral : 17.344 168.029 5889 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.46 % Favored : 90.47 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.12), residues: 4385 helix: -0.52 (0.10), residues: 2546 sheet: -3.04 (0.44), residues: 118 loop : -2.47 (0.15), residues: 1721 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 4.591 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: 1 outliers final: 1 residues processed: 246 average time/residue: 0.5146 time to fit residues: 212.6622 Evaluate side-chains 189 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 4.413 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3491 time to fit residues: 7.1606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 362 optimal weight: 2.9990 chunk 246 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 323 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 371 optimal weight: 6.9990 chunk 300 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN B 259 GLN B 484 GLN B 552 ASN C 303 GLN E 31 GLN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 453 ASN E 496 GLN ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 447 HIS ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 40020 Z= 0.208 Angle : 0.660 13.825 54610 Z= 0.352 Chirality : 0.042 0.224 6020 Planarity : 0.004 0.096 6548 Dihedral : 17.222 168.714 5889 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.96 % Favored : 90.97 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.78 (0.12), residues: 4385 helix: -0.28 (0.10), residues: 2571 sheet: -2.88 (0.45), residues: 114 loop : -2.43 (0.15), residues: 1700 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 4.954 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 outliers start: 1 outliers final: 1 residues processed: 248 average time/residue: 0.5207 time to fit residues: 216.9419 Evaluate side-chains 191 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 4.771 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3290 time to fit residues: 6.8138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 146 optimal weight: 1.9990 chunk 391 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 435 optimal weight: 2.9990 chunk 361 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 144 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 40020 Z= 0.231 Angle : 0.661 14.209 54610 Z= 0.353 Chirality : 0.042 0.234 6020 Planarity : 0.004 0.073 6548 Dihedral : 17.154 169.292 5889 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.33 % Favored : 90.60 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.63 (0.13), residues: 4385 helix: -0.16 (0.10), residues: 2578 sheet: -3.03 (0.48), residues: 97 loop : -2.39 (0.15), residues: 1710 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 4.833 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: 1 outliers final: 1 residues processed: 241 average time/residue: 0.5174 time to fit residues: 211.4348 Evaluate side-chains 191 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 4.599 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4208 time to fit residues: 6.9573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 419 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 317 optimal weight: 20.0000 chunk 246 optimal weight: 1.9990 chunk 366 optimal weight: 6.9990 chunk 243 optimal weight: 4.9990 chunk 433 optimal weight: 1.9990 chunk 271 optimal weight: 0.8980 chunk 264 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 256 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 40020 Z= 0.250 Angle : 0.678 13.954 54610 Z= 0.362 Chirality : 0.043 0.290 6020 Planarity : 0.004 0.078 6548 Dihedral : 17.124 170.109 5889 Min Nonbonded Distance : 1.577 Molprobity Statistics. All-atom Clashscore : 23.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.69 % Favored : 90.26 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.54 (0.13), residues: 4385 helix: -0.10 (0.10), residues: 2573 sheet: -3.02 (0.49), residues: 97 loop : -2.32 (0.15), residues: 1715 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 4.735 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 outliers start: 1 outliers final: 1 residues processed: 235 average time/residue: 0.5104 time to fit residues: 204.1113 Evaluate side-chains 184 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 4.915 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5803 time to fit residues: 8.1699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 268 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 259 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 275 optimal weight: 0.7980 chunk 295 optimal weight: 7.9990 chunk 214 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 340 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 256 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 40020 Z= 0.206 Angle : 0.651 13.574 54610 Z= 0.346 Chirality : 0.042 0.219 6020 Planarity : 0.004 0.067 6548 Dihedral : 17.052 170.461 5889 Min Nonbonded Distance : 1.497 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.14 % Favored : 90.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.44 (0.13), residues: 4385 helix: 0.01 (0.10), residues: 2582 sheet: -3.15 (0.41), residues: 137 loop : -2.28 (0.15), residues: 1666 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 4.590 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 outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.5052 time to fit residues: 205.3510 Evaluate side-chains 188 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 4.752 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 394 optimal weight: 6.9990 chunk 415 optimal weight: 0.0030 chunk 379 optimal weight: 9.9990 chunk 404 optimal weight: 0.0980 chunk 243 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 317 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 365 optimal weight: 7.9990 chunk 382 optimal weight: 4.9990 chunk 402 optimal weight: 2.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 303 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN C 211 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 339 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 HIS L 256 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 40020 Z= 0.168 Angle : 0.635 15.423 54610 Z= 0.335 Chirality : 0.042 0.241 6020 Planarity : 0.004 0.054 6548 Dihedral : 16.952 171.171 5889 Min Nonbonded Distance : 1.545 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.51 % Favored : 91.45 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.29 (0.13), residues: 4385 helix: 0.16 (0.10), residues: 2584 sheet: -2.90 (0.43), residues: 125 loop : -2.31 (0.15), residues: 1676 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 4.601 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 outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.5025 time to fit residues: 221.8588 Evaluate side-chains 194 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.907 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 265 optimal weight: 0.5980 chunk 427 optimal weight: 6.9990 chunk 260 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 297 optimal weight: 9.9990 chunk 448 optimal weight: 0.2980 chunk 412 optimal weight: 0.8980 chunk 356 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 275 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 40020 Z= 0.173 Angle : 0.641 15.458 54610 Z= 0.337 Chirality : 0.042 0.242 6020 Planarity : 0.004 0.052 6548 Dihedral : 16.858 172.159 5889 Min Nonbonded Distance : 1.498 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.32 % Favored : 91.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.24 (0.13), residues: 4385 helix: 0.20 (0.10), residues: 2588 sheet: -3.02 (0.42), residues: 127 loop : -2.28 (0.15), residues: 1670 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8770 Ramachandran restraints generated. 4385 Oldfield, 0 Emsley, 4385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 4.585 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 outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.5297 time to fit residues: 222.7506 Evaluate side-chains 192 residues out of total 4163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 4.721 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 283 optimal weight: 4.9990 chunk 380 optimal weight: 4.9990 chunk 109 optimal weight: 0.0970 chunk 329 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 chunk 357 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 367 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 overall best weight: 2.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN D 88 GLN ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN ** H 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.049617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.035390 restraints weight = 413205.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.036603 restraints weight = 269738.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.036889 restraints weight = 192438.237| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 40020 Z= 0.230 Angle : 0.668 13.852 54610 Z= 0.355 Chirality : 0.042 0.233 6020 Planarity : 0.004 0.053 6548 Dihedral : 16.837 172.947 5889 Min Nonbonded Distance : 1.337 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.99 % Favored : 90.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 4385 helix: 0.23 (0.10), residues: 2588 sheet: -3.06 (0.39), residues: 144 loop : -2.25 (0.15), residues: 1653 =============================================================================== Job complete usr+sys time: 6194.90 seconds wall clock time: 115 minutes 39.29 seconds (6939.29 seconds total)