Starting phenix.real_space_refine (version: dev) on Wed Dec 21 05:33:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hum_0281/12_2022/6hum_0281_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hum_0281/12_2022/6hum_0281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hum_0281/12_2022/6hum_0281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hum_0281/12_2022/6hum_0281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hum_0281/12_2022/6hum_0281_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hum_0281/12_2022/6hum_0281_updated.pdb" } resolution = 3.34 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12130 atoms to isotropic. 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 229": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "D TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 25": "NH1" <-> "NH2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 17": "NH1" <-> "NH2" Residue "J ARG 45": "NH1" <-> "NH2" Residue "J TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 26": "NH1" <-> "NH2" Residue "H TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "I TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 179": "NH1" <-> "NH2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 174": "NH1" <-> "NH2" Residue "L TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 35": "NH1" <-> "NH2" Residue "L ARG 72": "NH1" <-> "NH2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 211": "NH1" <-> "NH2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 388": "NH1" <-> "NH2" Residue "F TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 599": "NH1" <-> "NH2" Residue "F PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 32": "NH1" <-> "NH2" Residue "N ARG 35": "NH1" <-> "NH2" Residue "N ARG 136": "NH1" <-> "NH2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 6": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 29521 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2718 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3706 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 23, 'TRANS': 464} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 52 Chain: "E" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 769 Classifications: {'peptide': 100} Link IDs: {'TRANS': 99} Chain: "B" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3541 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 456} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "G" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1262 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 160} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1278 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 11, 'TRANS': 144} Chain: "P" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 39} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3153 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 370} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1520 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 180} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1594 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 184} 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: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 609 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "F" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4717 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 583} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "N" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1160 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 11, 'TRANS': 135} Chain: "M" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 879 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "S" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 432 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "O" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "Q" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 293 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'BCR': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18481 SG CYS I 103 47.382 91.207 38.473 1.00 26.35 S ATOM 18525 SG CYS I 109 44.242 93.994 33.933 1.00 28.75 S ATOM 18234 SG CYS I 73 46.157 97.062 39.909 1.00 28.05 S ATOM 18506 SG CYS I 106 41.768 93.980 39.802 1.00 27.85 S ATOM 18181 SG CYS I 66 44.541 103.300 28.434 1.00 32.87 S ATOM 18203 SG CYS I 69 46.002 99.047 31.191 1.00 30.30 S ATOM 18162 SG CYS I 63 49.829 100.629 25.719 1.00 35.29 S ATOM 18559 SG CYS I 113 43.654 97.644 26.474 1.00 31.80 S ATOM 20268 SG CYS K 148 45.749 88.119 47.073 1.00 27.27 S ATOM 19544 SG CYS K 53 46.363 82.991 50.147 1.00 29.75 S ATOM 19538 SG CYS K 52 41.606 84.909 50.781 1.00 30.22 S ATOM 20042 SG CYS K 117 46.734 89.806 50.339 1.00 26.68 S Time building chain proxies: 15.81, per 1000 atoms: 0.54 Number of scatterers: 29521 At special positions: 0 Unit cell: (97.2, 137.7, 243, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 168 16.00 O 5075 8.00 N 4758 7.00 C 19508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.05 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 201 " pdb=" FE1 SF4 I 201 " - pdb=" SG CYS I 103 " pdb=" FE4 SF4 I 201 " - pdb=" SG CYS I 106 " pdb=" FE3 SF4 I 201 " - pdb=" SG CYS I 73 " pdb=" FE2 SF4 I 201 " - pdb=" SG CYS I 109 " pdb=" SF4 I 202 " pdb=" FE1 SF4 I 202 " - pdb=" SG CYS I 66 " pdb=" FE2 SF4 I 202 " - pdb=" SG CYS I 69 " pdb=" FE3 SF4 I 202 " - pdb=" SG CYS I 63 " pdb=" FE4 SF4 I 202 " - pdb=" SG CYS I 113 " pdb=" SF4 K 501 " pdb=" FE4 SF4 K 501 " - pdb=" SG CYS K 117 " pdb=" FE3 SF4 K 501 " - pdb=" SG CYS K 52 " pdb=" FE2 SF4 K 501 " - pdb=" SG CYS K 53 " pdb=" FE1 SF4 K 501 " - pdb=" SG CYS K 148 " Number of angles added : 36 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6994 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 150 helices and 8 sheets defined 54.7% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 Processing helix chain 'A' and resid 22 through 28 Processing helix chain 'A' and resid 30 through 60 removed outlier: 3.614A pdb=" N MET A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 115 removed outlier: 3.977A pdb=" N THR A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 101 " --> pdb=" O TRP A 97 " (cutoff:3.500A) Proline residue: A 103 - end of helix Proline residue: A 109 - end of helix removed outlier: 4.155A pdb=" N TYR A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 151 removed outlier: 3.949A pdb=" N SER A 139 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.928A pdb=" N GLY A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.776A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 208 through 211 No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 215 through 224 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 252 through 276 Processing helix chain 'A' and resid 300 through 329 removed outlier: 3.776A pdb=" N ALA A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 341 No H-bonds generated for 'chain 'A' and resid 338 through 341' Processing helix chain 'A' and resid 348 through 365 Processing helix chain 'C' and resid 22 through 43 Proline residue: C 33 - end of helix removed outlier: 3.801A pdb=" N SER C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 90 removed outlier: 3.603A pdb=" N THR C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 101 removed outlier: 4.835A pdb=" N HIS C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLN C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 125 removed outlier: 3.876A pdb=" N ILE C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 23 Proline residue: D 14 - end of helix removed outlier: 3.984A pdb=" N ALA D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Proline residue: D 22 - end of helix Processing helix chain 'D' and resid 33 through 52 removed outlier: 3.783A pdb=" N TYR D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 103 Proline residue: D 90 - end of helix removed outlier: 3.941A pdb=" N THR D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 128 removed outlier: 3.947A pdb=" N LEU D 121 " --> pdb=" O TYR D 117 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE D 128 " --> pdb=" O TYR D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 155 removed outlier: 3.820A pdb=" N PHE D 140 " --> pdb=" O MET D 136 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LEU D 147 " --> pdb=" O TRP D 143 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 162 through 175 Processing helix chain 'D' and resid 179 through 188 Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.702A pdb=" N LEU D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LEU D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 240 removed outlier: 4.247A pdb=" N ASP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 removed outlier: 3.793A pdb=" N LEU D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 266 Processing helix chain 'D' and resid 271 through 298 removed outlier: 3.724A pdb=" N LYS D 276 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 303 through 322 removed outlier: 4.136A pdb=" N GLY D 315 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N PHE D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL D 317 " --> pdb=" O HIS D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 357 removed outlier: 3.698A pdb=" N LEU D 341 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA D 344 " --> pdb=" O GLY D 340 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 370 No H-bonds generated for 'chain 'D' and resid 368 through 370' Processing helix chain 'D' and resid 375 through 386 Processing helix chain 'D' and resid 393 through 407 removed outlier: 3.722A pdb=" N GLU D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 441 removed outlier: 3.874A pdb=" N VAL D 425 " --> pdb=" O PHE D 421 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) Proline residue: D 431 - end of helix Processing helix chain 'D' and resid 461 through 479 removed outlier: 3.594A pdb=" N ILE D 466 " --> pdb=" O ARG D 462 " (cutoff:3.500A) Proline residue: D 473 - end of helix Processing helix chain 'D' and resid 481 through 485 Processing helix chain 'D' and resid 489 through 501 Processing helix chain 'E' and resid 3 through 23 Processing helix chain 'E' and resid 28 through 51 removed outlier: 3.919A pdb=" N MET E 32 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 87 removed outlier: 3.529A pdb=" N ARG E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'B' and resid 16 through 37 removed outlier: 4.893A pdb=" N ILE B 20 " --> pdb=" O PRO B 17 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE B 34 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 37 " --> pdb=" O ILE B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 60 removed outlier: 4.071A pdb=" N ILE B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE B 59 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Proline residue: B 60 - end of helix Processing helix chain 'B' and resid 78 through 102 removed outlier: 5.493A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR B 101 " --> pdb=" O MET B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 128 removed outlier: 3.589A pdb=" N ALA B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 151 removed outlier: 3.845A pdb=" N GLY B 151 " --> pdb=" O TYR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 186 Processing helix chain 'B' and resid 197 through 200 No H-bonds generated for 'chain 'B' and resid 197 through 200' Processing helix chain 'B' and resid 206 through 223 removed outlier: 4.018A pdb=" N LYS B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 238 removed outlier: 4.478A pdb=" N ASP B 234 " --> pdb=" O GLN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 263 removed outlier: 3.903A pdb=" N VAL B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 292 removed outlier: 3.575A pdb=" N ASN B 290 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 Processing helix chain 'B' and resid 325 through 353 removed outlier: 3.715A pdb=" N PHE B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 362 Processing helix chain 'B' and resid 370 through 384 Processing helix chain 'B' and resid 390 through 405 Processing helix chain 'B' and resid 409 through 432 removed outlier: 4.464A pdb=" N TYR B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL B 428 " --> pdb=" O TYR B 424 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL B 429 " --> pdb=" O TYR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 442 through 445 No H-bonds generated for 'chain 'B' and resid 442 through 445' Processing helix chain 'B' and resid 458 through 473 removed outlier: 3.721A pdb=" N ALA B 470 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 490 removed outlier: 3.651A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 28 removed outlier: 3.807A pdb=" N GLN G 8 " --> pdb=" O ALA G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 53 removed outlier: 3.717A pdb=" N ILE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 52 " --> pdb=" O GLY G 48 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 65 Processing helix chain 'G' and resid 70 through 81 removed outlier: 3.981A pdb=" N MET G 79 " --> pdb=" O LEU G 75 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 115 removed outlier: 4.575A pdb=" N TRP G 94 " --> pdb=" O PRO G 91 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG G 96 " --> pdb=" O ARG G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 141 removed outlier: 3.685A pdb=" N PHE G 140 " --> pdb=" O GLY G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 164 removed outlier: 4.045A pdb=" N VAL G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 163 " --> pdb=" O ILE G 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 20 Processing helix chain 'J' and resid 44 through 55 removed outlier: 4.559A pdb=" N LEU J 47 " --> pdb=" O ASP J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 128 Processing helix chain 'J' and resid 162 through 164 No H-bonds generated for 'chain 'J' and resid 162 through 164' Processing helix chain 'P' and resid 5 through 25 Proline residue: P 14 - end of helix removed outlier: 3.899A pdb=" N THR P 25 " --> pdb=" O LEU P 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 56 removed outlier: 5.080A pdb=" N GLU H 56 " --> pdb=" O GLU H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 69 Proline residue: H 65 - end of helix removed outlier: 4.012A pdb=" N SER H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG H 69 " --> pdb=" O PRO H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 89 Proline residue: H 86 - end of helix removed outlier: 3.973A pdb=" N LEU H 89 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 123 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 129 through 134 Processing helix chain 'H' and resid 138 through 148 removed outlier: 3.722A pdb=" N TYR H 142 " --> pdb=" O ARG H 138 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 193 removed outlier: 4.619A pdb=" N VAL H 173 " --> pdb=" O TYR H 170 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR H 174 " --> pdb=" O GLY H 171 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS H 175 " --> pdb=" O TRP H 172 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE H 183 " --> pdb=" O CYS H 180 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU H 184 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Proline residue: H 185 - end of helix removed outlier: 3.999A pdb=" N ASP H 188 " --> pdb=" O PRO H 185 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR H 190 " --> pdb=" O VAL H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 203 removed outlier: 4.456A pdb=" N ARG H 203 " --> pdb=" O ILE H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 217 No H-bonds generated for 'chain 'H' and resid 214 through 217' Processing helix chain 'H' and resid 223 through 228 removed outlier: 3.876A pdb=" N SER H 228 " --> pdb=" O MET H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 237 No H-bonds generated for 'chain 'H' and resid 234 through 237' Processing helix chain 'H' and resid 258 through 282 removed outlier: 3.749A pdb=" N VAL H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG H 270 " --> pdb=" O ILE H 266 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL H 273 " --> pdb=" O MET H 269 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP H 281 " --> pdb=" O ARG H 277 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY H 282 " --> pdb=" O GLN H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 297 Processing helix chain 'H' and resid 303 through 305 No H-bonds generated for 'chain 'H' and resid 303 through 305' Processing helix chain 'H' and resid 307 through 309 No H-bonds generated for 'chain 'H' and resid 307 through 309' Processing helix chain 'H' and resid 358 through 366 removed outlier: 4.215A pdb=" N VAL H 365 " --> pdb=" O ASN H 361 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU H 366 " --> pdb=" O ASN H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 382 Processing helix chain 'H' and resid 389 through 392 Processing helix chain 'I' and resid 4 through 31 removed outlier: 3.838A pdb=" N GLY I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 72 Processing helix chain 'I' and resid 108 through 112 Processing helix chain 'I' and resid 138 through 140 No H-bonds generated for 'chain 'I' and resid 138 through 140' Processing helix chain 'I' and resid 160 through 162 No H-bonds generated for 'chain 'I' and resid 160 through 162' Processing helix chain 'I' and resid 184 through 192 Processing helix chain 'K' and resid 26 through 40 removed outlier: 3.630A pdb=" N LEU K 31 " --> pdb=" O ILE K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 61 Processing helix chain 'K' and resid 96 through 102 removed outlier: 4.301A pdb=" N LEU K 101 " --> pdb=" O ALA K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 125 Processing helix chain 'K' and resid 135 through 137 No H-bonds generated for 'chain 'K' and resid 135 through 137' Processing helix chain 'K' and resid 152 through 166 removed outlier: 3.621A pdb=" N MET K 156 " --> pdb=" O PRO K 152 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS K 165 " --> pdb=" O LYS K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 177 removed outlier: 4.036A pdb=" N ARG K 174 " --> pdb=" O ILE K 171 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLY K 175 " --> pdb=" O ASN K 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 20 Processing helix chain 'L' and resid 24 through 34 Processing helix chain 'L' and resid 42 through 53 Processing helix chain 'L' and resid 55 through 61 removed outlier: 4.331A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 27 Proline residue: F 12 - end of helix Proline residue: F 15 - end of helix removed outlier: 3.968A pdb=" N ILE F 27 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 38 through 64 Processing helix chain 'F' and resid 91 through 114 removed outlier: 3.774A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 139 removed outlier: 4.047A pdb=" N PHE F 125 " --> pdb=" O TYR F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 162 removed outlier: 4.040A pdb=" N ILE F 149 " --> pdb=" O GLN F 146 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE F 150 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL F 154 " --> pdb=" O TRP F 151 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE F 162 " --> pdb=" O TYR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 199 removed outlier: 3.878A pdb=" N ASN F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 217 removed outlier: 3.589A pdb=" N LEU F 212 " --> pdb=" O MET F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 240 removed outlier: 3.510A pdb=" N LEU F 232 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Proline residue: F 237 - end of helix Processing helix chain 'F' and resid 248 through 255 removed outlier: 4.043A pdb=" N ASP F 252 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET F 254 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU F 255 " --> pdb=" O PRO F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 270 through 284 removed outlier: 4.182A pdb=" N VAL F 274 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Proline residue: F 282 - end of helix Processing helix chain 'F' and resid 288 through 311 removed outlier: 4.248A pdb=" N THR F 292 " --> pdb=" O PRO F 288 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR F 293 " --> pdb=" O GLN F 289 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR F 311 " --> pdb=" O THR F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 335 removed outlier: 3.882A pdb=" N TYR F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 365 removed outlier: 4.813A pdb=" N TYR F 351 " --> pdb=" O MET F 347 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE F 352 " --> pdb=" O THR F 348 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F 353 " --> pdb=" O HIS F 349 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA F 354 " --> pdb=" O ALA F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 383 No H-bonds generated for 'chain 'F' and resid 381 through 383' Processing helix chain 'F' and resid 392 through 404 Processing helix chain 'F' and resid 412 through 426 removed outlier: 4.119A pdb=" N GLU F 419 " --> pdb=" O TRP F 415 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 420 " --> pdb=" O SER F 416 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEU F 421 " --> pdb=" O LYS F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 451 removed outlier: 3.779A pdb=" N PHE F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR F 450 " --> pdb=" O MET F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 503 Proline residue: F 489 - end of helix Proline residue: F 496 - end of helix removed outlier: 5.798A pdb=" N GLY F 501 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE F 502 " --> pdb=" O THR F 498 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL F 503 " --> pdb=" O LEU F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 514 No H-bonds generated for 'chain 'F' and resid 511 through 514' Processing helix chain 'F' and resid 534 through 555 removed outlier: 4.283A pdb=" N SER F 539 " --> pdb=" O ILE F 535 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER F 540 " --> pdb=" O LEU F 536 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 541 " --> pdb=" O GLY F 537 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET F 554 " --> pdb=" O VAL F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 589 Processing helix chain 'F' and resid 591 through 606 removed outlier: 3.524A pdb=" N ARG F 595 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG F 599 " --> pdb=" O ARG F 595 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL F 604 " --> pdb=" O GLN F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 610 through 630 removed outlier: 3.790A pdb=" N THR F 616 " --> pdb=" O VAL F 612 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY F 617 " --> pdb=" O VAL F 613 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY F 624 " --> pdb=" O THR F 620 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS F 628 " --> pdb=" O GLY F 624 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TYR F 629 " --> pdb=" O GLU F 625 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU F 630 " --> pdb=" O GLY F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 635 through 643 removed outlier: 4.124A pdb=" N LEU F 643 " --> pdb=" O ALA F 639 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 16 Processing helix chain 'N' and resid 31 through 38 Processing helix chain 'N' and resid 110 through 121 removed outlier: 4.299A pdb=" N GLN N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 57 Processing helix chain 'M' and resid 67 through 87 Processing helix chain 'S' and resid 92 through 94 No H-bonds generated for 'chain 'S' and resid 92 through 94' Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'Q' and resid 17 through 39 removed outlier: 3.981A pdb=" N LEU Q 26 " --> pdb=" O ILE Q 22 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 11 through 14 removed outlier: 3.624A pdb=" N ASP H 39 " --> pdb=" O THR H 31 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 327 through 332 Processing sheet with id= C, first strand: chain 'I' and resid 79 through 82 Processing sheet with id= D, first strand: chain 'K' and resid 83 through 87 removed outlier: 7.121A pdb=" N TYR K 110 " --> pdb=" O ILE K 84 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR K 86 " --> pdb=" O TYR K 110 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE K 112 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL K 143 " --> pdb=" O ALA K 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'F' and resid 74 through 77 removed outlier: 6.877A pdb=" N ILE F 83 " --> pdb=" O TRP F 75 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'N' and resid 18 through 21 removed outlier: 6.879A pdb=" N VAL N 128 " --> pdb=" O LEU N 19 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU N 21 " --> pdb=" O VAL N 128 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL N 130 " --> pdb=" O LEU N 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'S' and resid 50 through 52 removed outlier: 6.732A pdb=" N ALA S 76 " --> pdb=" O GLN S 68 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE S 70 " --> pdb=" O LYS S 74 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS S 86 " --> pdb=" O PHE S 79 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'O' and resid 59 through 61 removed outlier: 3.746A pdb=" N TYR O 47 " --> pdb=" O ARG O 44 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP O 42 " --> pdb=" O GLN O 49 " (cutoff:3.500A) 1286 hydrogen bonds defined for protein. 3555 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.68 Time building geometry restraints manager: 13.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 12575 1.42 - 1.64: 17395 1.64 - 1.85: 281 1.85 - 2.07: 0 2.07 - 2.28: 37 Bond restraints: 30288 Sorted by residual: bond pdb=" C ILE D 24 " pdb=" N PRO D 25 " ideal model delta sigma weight residual 1.334 2.241 -0.907 2.34e-02 1.83e+03 1.50e+03 bond pdb=" C GLN F 570 " pdb=" N PRO F 571 " ideal model delta sigma weight residual 1.332 1.365 -0.033 8.90e-03 1.26e+04 1.35e+01 bond pdb=" C LYS O 51 " pdb=" N PHE O 52 " ideal model delta sigma weight residual 1.331 1.394 -0.063 2.07e-02 2.33e+03 9.33e+00 bond pdb=" C GLN L 70 " pdb=" N PRO L 71 " ideal model delta sigma weight residual 1.331 1.366 -0.035 1.27e-02 6.20e+03 7.66e+00 bond pdb=" C PRO J 91 " pdb=" N PRO J 92 " ideal model delta sigma weight residual 1.336 1.368 -0.032 1.20e-02 6.94e+03 7.27e+00 ... (remaining 30283 not shown) Histogram of bond angle deviations from ideal: 12.73 - 38.28: 1 38.28 - 63.82: 0 63.82 - 89.36: 36 89.36 - 114.91: 18579 114.91 - 140.45: 22656 Bond angle restraints: 41272 Sorted by residual: angle pdb=" O ILE D 24 " pdb=" C ILE D 24 " pdb=" N PRO D 25 " ideal model delta sigma weight residual 121.10 12.73 108.37 1.14e+00 7.69e-01 9.04e+03 angle pdb=" C ALA O 22 " pdb=" N LEU O 23 " pdb=" CA LEU O 23 " ideal model delta sigma weight residual 120.63 140.45 -19.82 1.61e+00 3.86e-01 1.52e+02 angle pdb=" O PHE D 23 " pdb=" C PHE D 23 " pdb=" N ILE D 24 " ideal model delta sigma weight residual 122.59 109.25 13.34 1.33e+00 5.65e-01 1.01e+02 angle pdb=" C TYR O 47 " pdb=" N ALA O 48 " pdb=" CA ALA O 48 " ideal model delta sigma weight residual 122.94 134.62 -11.68 1.50e+00 4.44e-01 6.07e+01 angle pdb=" N ASP J 32 " pdb=" CA ASP J 32 " pdb=" C ASP J 32 " ideal model delta sigma weight residual 112.26 121.64 -9.38 1.32e+00 5.74e-01 5.05e+01 ... (remaining 41267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 17167 23.82 - 47.64: 439 47.64 - 71.46: 30 71.46 - 95.28: 15 95.28 - 119.11: 1 Dihedral angle restraints: 17652 sinusoidal: 6725 harmonic: 10927 Sorted by residual: dihedral pdb=" CA CYS K 148 " pdb=" C CYS K 148 " pdb=" N PRO K 149 " pdb=" CA PRO K 149 " ideal model delta harmonic sigma weight residual -180.00 -116.41 -63.59 0 5.00e+00 4.00e-02 1.62e+02 dihedral pdb=" CA PRO B 387 " pdb=" C PRO B 387 " pdb=" N PRO B 388 " pdb=" CA PRO B 388 " ideal model delta harmonic sigma weight residual -180.00 -117.52 -62.48 0 5.00e+00 4.00e-02 1.56e+02 dihedral pdb=" CA LEU C 16 " pdb=" C LEU C 16 " pdb=" N SER C 17 " pdb=" CA SER C 17 " ideal model delta harmonic sigma weight residual -180.00 -142.51 -37.49 0 5.00e+00 4.00e-02 5.62e+01 ... (remaining 17649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.348: 4755 0.348 - 0.696: 18 0.696 - 1.044: 0 1.044 - 1.392: 1 1.392 - 1.740: 10 Chirality restraints: 4784 Sorted by residual: chirality pdb=" CG LEU O 33 " pdb=" CB LEU O 33 " pdb=" CD1 LEU O 33 " pdb=" CD2 LEU O 33 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.57e+01 chirality pdb=" CG LEU M 29 " pdb=" CB LEU M 29 " pdb=" CD1 LEU M 29 " pdb=" CD2 LEU M 29 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.53e+01 chirality pdb=" CG LEU J 75 " pdb=" CB LEU J 75 " pdb=" CD1 LEU J 75 " pdb=" CD2 LEU J 75 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.36e+01 ... (remaining 4781 not shown) Planarity restraints: 5110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BCR D 601 " -0.503 2.00e-02 2.50e+03 3.29e-01 1.36e+03 pdb=" C11 BCR D 601 " 0.387 2.00e-02 2.50e+03 pdb=" C34 BCR D 601 " 0.079 2.00e-02 2.50e+03 pdb=" C8 BCR D 601 " 0.276 2.00e-02 2.50e+03 pdb=" C9 BCR D 601 " -0.240 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 BCR D 601 " 0.229 2.00e-02 2.50e+03 2.00e-01 4.98e+02 pdb=" C17 BCR D 601 " -0.362 2.00e-02 2.50e+03 pdb=" C18 BCR D 601 " 0.024 2.00e-02 2.50e+03 pdb=" C19 BCR D 601 " 0.124 2.00e-02 2.50e+03 pdb=" C36 BCR D 601 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 BCR D 601 " 0.161 2.00e-02 2.50e+03 1.81e-01 3.28e+02 pdb=" C23 BCR D 601 " -0.115 2.00e-02 2.50e+03 pdb=" C24 BCR D 601 " -0.236 2.00e-02 2.50e+03 pdb=" C25 BCR D 601 " 0.190 2.00e-02 2.50e+03 ... (remaining 5107 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 11 2.02 - 2.74: 3088 2.74 - 3.46: 44626 3.46 - 4.18: 69945 4.18 - 4.90: 128449 Nonbonded interactions: 246119 Sorted by model distance: nonbonded pdb=" CG ARG D 356 " pdb=" CB LEU D 456 " model vdw 1.302 3.840 nonbonded pdb=" CE1 PHE H 153 " pdb=" OE2 GLU K 56 " model vdw 1.460 3.340 nonbonded pdb=" OG1 THR M 7 " pdb=" OE2 GLU M 78 " model vdw 1.508 2.440 nonbonded pdb=" CG2 THR D 233 " pdb=" OD1 ASP F 610 " model vdw 1.684 3.460 nonbonded pdb=" OD2 ASP J 32 " pdb=" NH1 ARG J 95 " model vdw 1.731 2.520 ... (remaining 246114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 168 5.16 5 C 19508 2.51 5 N 4758 2.21 5 O 5075 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 8.200 Check model and map are aligned: 0.380 Convert atoms to be neutral: 0.220 Process input model: 76.050 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.009 0.907 30288 Z= 0.619 Angle : 1.204 108.368 41272 Z= 0.738 Chirality : 0.098 1.740 4784 Planarity : 0.010 0.329 5110 Dihedral : 10.915 119.106 10658 Min Nonbonded Distance : 1.302 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.67 % Allowed : 11.47 % Favored : 87.86 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.11 % 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: -4.32 (0.12), residues: 3739 helix: -2.07 (0.10), residues: 2105 sheet: -3.97 (0.34), residues: 152 loop : -3.89 (0.14), residues: 1482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7478 Ramachandran restraints generated. 3739 Oldfield, 0 Emsley, 3739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 773 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 781 average time/residue: 0.4401 time to fit residues: 548.0448 Evaluate side-chains 565 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 557 time to evaluate : 3.469 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2775 time to fit residues: 8.9204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 189 optimal weight: 0.2980 chunk 150 optimal weight: 0.4980 chunk 290 optimal weight: 0.0970 chunk 112 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 336 optimal weight: 0.6980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS C 100 GLN D 326 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN G 71 ASN G 121 GLN ** J 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 27 ASN H 18 HIS H 60 ASN H 205 GLN ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN I 85 ASN I 178 GLN K 76 ASN K 104 GLN F 6 GLN F 66 HIS F 509 ASN M 32 ASN M 59 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 30288 Z= 0.219 Angle : 0.753 11.104 41272 Z= 0.368 Chirality : 0.045 0.254 4784 Planarity : 0.006 0.069 5110 Dihedral : 7.439 101.219 4143 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.32 % Favored : 89.47 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.08 % 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: -2.99 (0.13), residues: 3741 helix: -0.84 (0.11), residues: 2116 sheet: -3.50 (0.35), residues: 157 loop : -3.56 (0.15), residues: 1468 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 650 time to evaluate : 3.157 Fit side-chains outliers start: 67 outliers final: 32 residues processed: 680 average time/residue: 0.3885 time to fit residues: 429.3872 Evaluate side-chains 583 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 551 time to evaluate : 3.331 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2891 time to fit residues: 21.4559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 187 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 280 optimal weight: 0.8980 chunk 229 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 337 optimal weight: 1.9990 chunk 364 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 334 optimal weight: 0.0030 chunk 115 optimal weight: 0.5980 chunk 270 optimal weight: 0.4980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS D 65 GLN D 326 ASN E 50 ASN B 273 GLN B 290 ASN J 20 GLN J 73 GLN J 120 GLN ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 ASN I 85 ASN I 178 GLN K 104 GLN K 203 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 30288 Z= 0.217 Angle : 0.707 9.839 41272 Z= 0.346 Chirality : 0.044 0.261 4784 Planarity : 0.005 0.068 5110 Dihedral : 6.752 87.758 4143 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.60 % Favored : 90.19 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.14), residues: 3741 helix: -0.29 (0.11), residues: 2127 sheet: -3.09 (0.36), residues: 183 loop : -3.28 (0.15), residues: 1431 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 645 time to evaluate : 3.242 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 28 residues processed: 690 average time/residue: 0.3937 time to fit residues: 439.7082 Evaluate side-chains 602 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 574 time to evaluate : 3.129 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2601 time to fit residues: 18.0564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 333 optimal weight: 4.9990 chunk 253 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 338 optimal weight: 2.9990 chunk 358 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 321 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS C 100 GLN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN E 87 ASN B 191 HIS B 290 ASN G 117 GLN J 20 GLN J 80 HIS P 27 ASN H 48 HIS H 84 ASN H 155 ASN ** H 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 ASN H 310 GLN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN F 66 HIS ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 HIS ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.070 30288 Z= 0.447 Angle : 0.838 10.203 41272 Z= 0.415 Chirality : 0.050 0.249 4784 Planarity : 0.006 0.075 5110 Dihedral : 7.030 88.919 4143 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.44 % Favored : 88.35 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.06 % 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: -2.23 (0.14), residues: 3741 helix: -0.29 (0.11), residues: 2130 sheet: -3.07 (0.37), residues: 177 loop : -3.12 (0.15), residues: 1434 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 707 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 48 residues processed: 767 average time/residue: 0.4093 time to fit residues: 511.9261 Evaluate side-chains 681 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 633 time to evaluate : 3.413 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.2990 time to fit residues: 31.7331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 298 optimal weight: 0.5980 chunk 203 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 147 optimal weight: 0.0030 chunk 306 optimal weight: 0.4980 chunk 247 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 183 optimal weight: 0.0470 chunk 321 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN D 134 GLN D 299 GLN D 326 ASN D 494 GLN B 290 ASN G 71 ASN G 117 GLN J 20 GLN J 120 GLN J 137 ASN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 ASN F 62 GLN ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 HIS F 313 ASN F 632 ASN M 37 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 30288 Z= 0.182 Angle : 0.693 9.956 41272 Z= 0.339 Chirality : 0.044 0.269 4784 Planarity : 0.005 0.068 5110 Dihedral : 6.404 89.277 4143 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.01 % Favored : 90.78 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.06 % 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: -1.76 (0.14), residues: 3741 helix: 0.12 (0.12), residues: 2125 sheet: -2.90 (0.40), residues: 161 loop : -2.96 (0.15), residues: 1455 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 671 time to evaluate : 2.929 Fit side-chains outliers start: 60 outliers final: 21 residues processed: 699 average time/residue: 0.3958 time to fit residues: 449.5988 Evaluate side-chains 607 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 586 time to evaluate : 3.110 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2695 time to fit residues: 15.0607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 120 optimal weight: 2.9990 chunk 322 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 358 optimal weight: 1.9990 chunk 297 optimal weight: 0.2980 chunk 166 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN G 71 ASN P 27 ASN H 156 ASN H 197 ASN H 327 HIS I 178 GLN F 62 GLN F 247 HIS F 312 GLN M 37 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 30288 Z= 0.270 Angle : 0.715 11.858 41272 Z= 0.349 Chirality : 0.045 0.236 4784 Planarity : 0.005 0.069 5110 Dihedral : 6.352 89.515 4143 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.40 % Favored : 89.39 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.06 % 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: -1.69 (0.14), residues: 3741 helix: 0.16 (0.12), residues: 2126 sheet: -2.64 (0.42), residues: 158 loop : -2.94 (0.15), residues: 1457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 618 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 30 residues processed: 650 average time/residue: 0.4001 time to fit residues: 421.3065 Evaluate side-chains 620 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 590 time to evaluate : 3.374 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2643 time to fit residues: 19.4158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 346 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 204 optimal weight: 0.3980 chunk 262 optimal weight: 0.8980 chunk 203 optimal weight: 0.9980 chunk 302 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 357 optimal weight: 1.9990 chunk 223 optimal weight: 0.5980 chunk 218 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN P 27 ASN I 178 GLN F 247 HIS F 632 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 30288 Z= 0.219 Angle : 0.699 11.730 41272 Z= 0.339 Chirality : 0.045 0.314 4784 Planarity : 0.005 0.068 5110 Dihedral : 6.238 89.679 4143 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.68 % Favored : 90.16 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3741 helix: 0.32 (0.12), residues: 2122 sheet: -2.61 (0.42), residues: 159 loop : -2.82 (0.15), residues: 1460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 616 time to evaluate : 3.215 Fit side-chains outliers start: 45 outliers final: 21 residues processed: 639 average time/residue: 0.4127 time to fit residues: 428.1203 Evaluate side-chains 607 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 586 time to evaluate : 3.251 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2762 time to fit residues: 15.4109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 221 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 213 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 281 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN F 247 HIS ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 30288 Z= 0.245 Angle : 0.698 10.711 41272 Z= 0.341 Chirality : 0.045 0.278 4784 Planarity : 0.005 0.099 5110 Dihedral : 6.222 89.592 4143 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.10 % Favored : 89.76 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3741 helix: 0.39 (0.12), residues: 2125 sheet: -2.58 (0.41), residues: 164 loop : -2.81 (0.16), residues: 1452 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 621 time to evaluate : 3.137 Fit side-chains outliers start: 43 outliers final: 20 residues processed: 641 average time/residue: 0.4128 time to fit residues: 427.3693 Evaluate side-chains 613 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 593 time to evaluate : 3.312 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2989 time to fit residues: 15.6741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 325 optimal weight: 0.4980 chunk 342 optimal weight: 0.6980 chunk 312 optimal weight: 1.9990 chunk 333 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 301 optimal weight: 0.7980 chunk 315 optimal weight: 0.6980 chunk 332 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 27 ASN I 178 GLN F 54 HIS F 632 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 30288 Z= 0.240 Angle : 0.702 10.517 41272 Z= 0.342 Chirality : 0.045 0.266 4784 Planarity : 0.005 0.102 5110 Dihedral : 6.220 89.466 4143 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.78 % Favored : 90.06 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.06 % 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: -1.32 (0.14), residues: 3741 helix: 0.44 (0.12), residues: 2133 sheet: -2.50 (0.43), residues: 159 loop : -2.75 (0.16), residues: 1449 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 621 time to evaluate : 3.369 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 639 average time/residue: 0.4112 time to fit residues: 426.4773 Evaluate side-chains 621 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 605 time to evaluate : 3.420 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2982 time to fit residues: 13.6817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 218 optimal weight: 0.6980 chunk 352 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 167 optimal weight: 0.0270 chunk 244 optimal weight: 2.9990 chunk 369 optimal weight: 0.5980 chunk 340 optimal weight: 0.6980 chunk 294 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS I 178 GLN F 217 ASN F 313 ASN F 632 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 30288 Z= 0.224 Angle : 0.704 12.669 41272 Z= 0.341 Chirality : 0.045 0.301 4784 Planarity : 0.005 0.102 5110 Dihedral : 6.175 89.358 4143 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.08 % Favored : 89.82 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3741 helix: 0.51 (0.12), residues: 2132 sheet: -2.48 (0.43), residues: 160 loop : -2.72 (0.16), residues: 1449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7482 Ramachandran restraints generated. 3741 Oldfield, 0 Emsley, 3741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 632 time to evaluate : 3.244 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 639 average time/residue: 0.4122 time to fit residues: 428.7148 Evaluate side-chains 606 residues out of total 3122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 597 time to evaluate : 3.240 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2893 time to fit residues: 9.2991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 233 optimal weight: 0.8980 chunk 313 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 271 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 302 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 ASN C 99 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN F 182 ASN F 217 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.132250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.109967 restraints weight = 38596.987| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.63 r_work: 0.3010 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 30288 Z= 0.234 Angle : 0.712 14.082 41272 Z= 0.345 Chirality : 0.045 0.254 4784 Planarity : 0.005 0.103 5110 Dihedral : 6.168 88.907 4143 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.92 % Favored : 89.92 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3741 helix: 0.52 (0.12), residues: 2139 sheet: -2.48 (0.42), residues: 160 loop : -2.74 (0.16), residues: 1442 =============================================================================== Job complete usr+sys time: 8079.14 seconds wall clock time: 144 minutes 38.40 seconds (8678.40 seconds total)