Starting phenix.real_space_refine (version: dev) on Sun Feb 26 07:35:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d45_30570/02_2023/7d45_30570_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d45_30570/02_2023/7d45_30570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d45_30570/02_2023/7d45_30570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d45_30570/02_2023/7d45_30570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d45_30570/02_2023/7d45_30570_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d45_30570/02_2023/7d45_30570_updated.pdb" } resolution = 3.8 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= 0.003 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 Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C ASP 219": "OD1" <-> "OD2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 219": "OD1" <-> "OD2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 301": "OD1" <-> "OD2" Residue "E PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E ASP 111": "OD1" <-> "OD2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E ARG 286": "NH1" <-> "NH2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "F ASP 111": "OD1" <-> "OD2" Residue "F TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 125": "OD1" <-> "OD2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 286": "NH1" <-> "NH2" Residue "F ASP 288": "OD1" <-> "OD2" Residue "F GLU 291": "OE1" <-> "OE2" Residue "G ASP 239": "OD1" <-> "OD2" Residue "G TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 344": "NH1" <-> "NH2" Residue "G PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 362": "OD1" <-> "OD2" Residue "G TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 417": "NH1" <-> "NH2" Residue "G GLU 445": "OE1" <-> "OE2" Residue "G ARG 446": "NH1" <-> "NH2" Residue "G ASP 458": "OD1" <-> "OD2" Residue "G GLU 469": "OE1" <-> "OE2" Residue "G GLU 495": "OE1" <-> "OE2" Residue "G ASP 498": "OD1" <-> "OD2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "H TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 344": "NH1" <-> "NH2" Residue "H ASP 362": "OD1" <-> "OD2" Residue "H TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 417": "NH1" <-> "NH2" Residue "H ARG 446": "NH1" <-> "NH2" Residue "H PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 456": "OE1" <-> "OE2" Residue "H ASP 458": "OD1" <-> "OD2" Residue "H ASP 490": "OD1" <-> "OD2" Residue "H ARG 517": "NH1" <-> "NH2" Residue "I PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 65": "NH1" <-> "NH2" Residue "I TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 154": "OD1" <-> "OD2" Residue "I ASP 199": "OD1" <-> "OD2" Residue "I PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 269": "NH1" <-> "NH2" Residue "I GLU 295": "OE1" <-> "OE2" Residue "I ARG 299": "NH1" <-> "NH2" Residue "I TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 455": "OD1" <-> "OD2" Residue "I GLU 458": "OE1" <-> "OE2" Residue "J ARG 65": "NH1" <-> "NH2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 133": "OD1" <-> "OD2" Residue "J ARG 195": "NH1" <-> "NH2" Residue "J ARG 211": "NH1" <-> "NH2" Residue "J PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 265": "OD1" <-> "OD2" Residue "J ARG 269": "NH1" <-> "NH2" Residue "J GLU 281": "OE1" <-> "OE2" Residue "J ARG 299": "NH1" <-> "NH2" Residue "J TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 316": "NH1" <-> "NH2" Residue "J GLU 357": "OE1" <-> "OE2" Residue "J PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 421": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 27529 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2265 Classifications: {'peptide': 293} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2256 Classifications: {'peptide': 291} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2476 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2515 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2445 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 11, 'TRANS': 334} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "F" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2465 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 12, 'TRANS': 337} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "H" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "I" Number of atoms: 3355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3355 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 408} 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: "J" Number of atoms: 3363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3363 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 409} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 889 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 18, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 340 Time building chain proxies: 15.14, per 1000 atoms: 0.55 Number of scatterers: 27529 At special positions: 0 Unit cell: (164.64, 167.58, 163.17, 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) S 142 16.00 P 1 15.00 O 5152 8.00 N 4827 7.00 C 17407 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: 11.54 Conformation dependent library (CDL) restraints added in 5.1 seconds 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6938 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 36 sheets defined 34.9% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.646A pdb=" N ALA A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 88 through 115 removed outlier: 4.670A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.871A pdb=" N ALA A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 4.826A pdb=" N LEU A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 189 removed outlier: 4.006A pdb=" N GLY A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE A 186 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET A 187 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 removed outlier: 4.011A pdb=" N ASN A 213 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN A 214 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 219 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 251 No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 46 through 59 removed outlier: 3.728A pdb=" N SER B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 76 Processing helix chain 'B' and resid 87 through 115 removed outlier: 3.926A pdb=" N LYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASN B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 161 through 171 removed outlier: 4.021A pdb=" N LEU B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 4.864A pdb=" N GLU B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.983A pdb=" N ASN B 213 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN B 214 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.503A pdb=" N LYS B 302 " --> pdb=" O GLU B 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 303 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 31 through 48 Processing helix chain 'C' and resid 54 through 71 Processing helix chain 'C' and resid 77 through 95 Processing helix chain 'C' and resid 129 through 158 removed outlier: 3.845A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HIS C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.668A pdb=" N ALA C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 210 removed outlier: 4.351A pdb=" N ALA C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 225 removed outlier: 4.559A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.885A pdb=" N HIS C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 303 No H-bonds generated for 'chain 'C' and resid 301 through 303' Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 55 through 71 removed outlier: 4.076A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 96 Processing helix chain 'D' and resid 128 through 145 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 172 through 183 removed outlier: 4.563A pdb=" N ARG D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 210 removed outlier: 3.796A pdb=" N ALA D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 297 through 299 No H-bonds generated for 'chain 'D' and resid 297 through 299' Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 333 through 343 removed outlier: 4.749A pdb=" N TYR D 337 " --> pdb=" O SER D 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 44 Proline residue: E 39 - end of helix Processing helix chain 'E' and resid 63 through 66 No H-bonds generated for 'chain 'E' and resid 63 through 66' Processing helix chain 'E' and resid 86 through 96 Proline residue: E 95 - end of helix Processing helix chain 'E' and resid 115 through 123 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'E' and resid 209 through 217 Processing helix chain 'E' and resid 229 through 237 removed outlier: 4.927A pdb=" N PHE E 237 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 4.330A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU E 293 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER E 294 " --> pdb=" O TRP E 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 45 Proline residue: F 39 - end of helix removed outlier: 4.053A pdb=" N ARG F 45 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 96 Proline residue: F 95 - end of helix Processing helix chain 'F' and resid 114 through 124 Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'F' and resid 224 through 227 No H-bonds generated for 'chain 'F' and resid 224 through 227' Processing helix chain 'F' and resid 229 through 235 Processing helix chain 'F' and resid 278 through 291 removed outlier: 4.130A pdb=" N ASN F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TRP F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 192 through 195 Processing helix chain 'G' and resid 205 through 215 Processing helix chain 'G' and resid 222 through 238 Processing helix chain 'G' and resid 248 through 266 removed outlier: 4.414A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 271 through 285 Processing helix chain 'G' and resid 293 through 311 Processing helix chain 'G' and resid 314 through 325 removed outlier: 4.112A pdb=" N GLN G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 350 Processing helix chain 'G' and resid 370 through 379 removed outlier: 4.344A pdb=" N ALA G 379 " --> pdb=" O SER G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 394 removed outlier: 4.415A pdb=" N SER G 392 " --> pdb=" O PRO G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 430 Processing helix chain 'G' and resid 460 through 463 Processing helix chain 'G' and resid 510 through 516 Proline residue: G 513 - end of helix removed outlier: 3.801A pdb=" N LEU G 516 " --> pdb=" O PRO G 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 510 through 516' Processing helix chain 'H' and resid 178 through 180 No H-bonds generated for 'chain 'H' and resid 178 through 180' Processing helix chain 'H' and resid 192 through 195 Processing helix chain 'H' and resid 205 through 215 Processing helix chain 'H' and resid 222 through 238 Processing helix chain 'H' and resid 248 through 266 removed outlier: 4.638A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 271 through 286 removed outlier: 3.636A pdb=" N SER H 286 " --> pdb=" O LYS H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 311 Processing helix chain 'H' and resid 314 through 323 Processing helix chain 'H' and resid 341 through 351 Processing helix chain 'H' and resid 369 through 377 Processing helix chain 'H' and resid 388 through 396 removed outlier: 5.169A pdb=" N SER H 392 " --> pdb=" O PRO H 389 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU H 395 " --> pdb=" O SER H 392 " (cutoff:3.500A) Proline residue: H 396 - end of helix Processing helix chain 'H' and resid 420 through 429 Processing helix chain 'H' and resid 460 through 462 No H-bonds generated for 'chain 'H' and resid 460 through 462' Processing helix chain 'H' and resid 509 through 511 No H-bonds generated for 'chain 'H' and resid 509 through 511' Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 75 through 86 removed outlier: 3.514A pdb=" N THR I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 107 Processing helix chain 'I' and resid 132 through 141 Processing helix chain 'I' and resid 162 through 175 Processing helix chain 'I' and resid 197 through 199 No H-bonds generated for 'chain 'I' and resid 197 through 199' Processing helix chain 'I' and resid 228 through 231 Processing helix chain 'I' and resid 254 through 262 removed outlier: 3.761A pdb=" N THR I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 278 Processing helix chain 'I' and resid 303 through 314 Processing helix chain 'I' and resid 339 through 341 No H-bonds generated for 'chain 'I' and resid 339 through 341' Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 65 through 67 No H-bonds generated for 'chain 'J' and resid 65 through 67' Processing helix chain 'J' and resid 75 through 85 Processing helix chain 'J' and resid 99 through 107 Processing helix chain 'J' and resid 131 through 141 Processing helix chain 'J' and resid 162 through 175 removed outlier: 3.712A pdb=" N GLU J 175 " --> pdb=" O ARG J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 234 Processing helix chain 'J' and resid 254 through 262 Processing helix chain 'J' and resid 269 through 276 Processing helix chain 'J' and resid 303 through 313 Processing helix chain 'J' and resid 339 through 341 No H-bonds generated for 'chain 'J' and resid 339 through 341' Processing helix chain 'K' and resid 53 through 55 No H-bonds generated for 'chain 'K' and resid 53 through 55' Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 91 through 117 Processing helix chain 'K' and resid 123 through 138 Processing helix chain 'K' and resid 147 through 156 removed outlier: 5.393A pdb=" N VAL K 156 " --> pdb=" O PHE K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 179 Processing sheet with id= A, first strand: chain 'A' and resid 289 through 291 removed outlier: 4.150A pdb=" N LEU A 283 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 192 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER A 149 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR A 127 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR A 151 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 206 through 208 Processing sheet with id= C, first strand: chain 'B' and resid 124 through 127 removed outlier: 6.061A pdb=" N SER B 149 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR B 127 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR B 151 " --> pdb=" O THR B 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 192 through 195 removed outlier: 7.448A pdb=" N VAL B 195 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B 227 " --> pdb=" O VAL B 195 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 284 through 286 Processing sheet with id= F, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.557A pdb=" N HIS C 188 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR C 167 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE C 190 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 232 through 234 removed outlier: 3.561A pdb=" N THR C 322 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL C 267 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N PHE C 324 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 246 through 248 Processing sheet with id= I, first strand: chain 'D' and resid 189 through 193 Processing sheet with id= J, first strand: chain 'D' and resid 231 through 234 removed outlier: 7.422A pdb=" N ILE D 234 " --> pdb=" O PRO D 264 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE D 266 " --> pdb=" O ILE D 234 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 245 through 248 Processing sheet with id= L, first strand: chain 'D' and resid 324 through 326 Processing sheet with id= M, first strand: chain 'E' and resid 205 through 207 removed outlier: 7.239A pdb=" N TYR E 264 " --> pdb=" O MET E 130 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET E 132 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE E 266 " --> pdb=" O MET E 132 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 193 through 196 removed outlier: 6.051A pdb=" N ASP E 161 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU E 167 " --> pdb=" O ASP E 161 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 362 through 364 removed outlier: 6.852A pdb=" N CYS E 379 " --> pdb=" O GLN E 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'F' and resid 3 through 8 removed outlier: 7.172A pdb=" N ASP F 100 " --> pdb=" O GLN F 4 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL F 6 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU F 102 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N MET F 8 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU F 104 " --> pdb=" O MET F 8 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 52 through 55 removed outlier: 7.037A pdb=" N VAL F 76 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N THR F 55 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE F 78 " --> pdb=" O THR F 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 194 through 196 removed outlier: 3.556A pdb=" N PHE F 157 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA F 171 " --> pdb=" O PHE F 157 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 352 through 354 Processing sheet with id= T, first strand: chain 'G' and resid 332 through 334 removed outlier: 6.287A pdb=" N ARG G 357 " --> pdb=" O ILE G 333 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'G' and resid 360 through 362 Processing sheet with id= V, first strand: chain 'G' and resid 414 through 416 Processing sheet with id= W, first strand: chain 'G' and resid 435 through 437 removed outlier: 5.586A pdb=" N LEU G 499 " --> pdb=" O VAL G 436 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 333 through 336 Processing sheet with id= Y, first strand: chain 'H' and resid 414 through 416 Processing sheet with id= Z, first strand: chain 'H' and resid 500 through 502 Processing sheet with id= AA, first strand: chain 'I' and resid 90 through 94 removed outlier: 6.167A pdb=" N LEU I 149 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL I 48 " --> pdb=" O LEU I 149 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL I 151 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 155 through 157 Processing sheet with id= AC, first strand: chain 'I' and resid 288 through 292 removed outlier: 3.572A pdb=" N GLU I 187 " --> pdb=" O THR I 292 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 238 through 241 removed outlier: 5.728A pdb=" N ASP I 206 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL I 212 " --> pdb=" O ASP I 206 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 373 through 375 Processing sheet with id= AF, first strand: chain 'J' and resid 155 through 157 Processing sheet with id= AG, first strand: chain 'J' and resid 238 through 241 removed outlier: 5.328A pdb=" N ASP J 206 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL J 212 " --> pdb=" O ASP J 206 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 373 through 375 Processing sheet with id= AI, first strand: chain 'K' and resid 18 through 21 removed outlier: 6.907A pdb=" N ASP K 83 " --> pdb=" O ILE K 73 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL K 75 " --> pdb=" O TYR K 81 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR K 81 " --> pdb=" O VAL K 75 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'K' and resid 41 through 46 removed outlier: 3.906A pdb=" N SER K 25 " --> pdb=" O TYR K 32 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER K 34 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL K 23 " --> pdb=" O SER K 34 " (cutoff:3.500A) 901 hydrogen bonds defined for protein. 2472 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: 8.67 Time building geometry restraints manager: 12.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9217 1.34 - 1.46: 4840 1.46 - 1.58: 13726 1.58 - 1.70: 4 1.70 - 1.82: 216 Bond restraints: 28003 Sorted by residual: bond pdb=" CA ALA G 349 " pdb=" C ALA G 349 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.31e-02 5.83e+03 1.74e+01 bond pdb=" CA LEU C 96 " pdb=" C LEU C 96 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.48e-02 4.57e+03 1.03e+01 bond pdb=" CA ARG J 121 " pdb=" CB ARG J 121 " ideal model delta sigma weight residual 1.524 1.483 0.041 1.33e-02 5.65e+03 9.40e+00 bond pdb=" CA ALA D 258 " pdb=" C ALA D 258 " ideal model delta sigma weight residual 1.523 1.485 0.039 1.34e-02 5.57e+03 8.30e+00 bond pdb=" C SER C 275 " pdb=" N PRO C 276 " ideal model delta sigma weight residual 1.331 1.309 0.022 7.90e-03 1.60e+04 7.97e+00 ... (remaining 27998 not shown) Histogram of bond angle deviations from ideal: 97.61 - 105.22: 497 105.22 - 112.82: 15668 112.82 - 120.43: 11352 120.43 - 128.04: 10303 128.04 - 135.65: 205 Bond angle restraints: 38025 Sorted by residual: angle pdb=" C THR G 241 " pdb=" N THR G 242 " pdb=" CA THR G 242 " ideal model delta sigma weight residual 122.67 104.49 18.18 2.19e+00 2.09e-01 6.89e+01 angle pdb=" N VAL J 178 " pdb=" CA VAL J 178 " pdb=" C VAL J 178 " ideal model delta sigma weight residual 113.53 106.31 7.22 9.80e-01 1.04e+00 5.42e+01 angle pdb=" N PRO F 24 " pdb=" CA PRO F 24 " pdb=" CB PRO F 24 " ideal model delta sigma weight residual 103.25 110.96 -7.71 1.05e+00 9.07e-01 5.39e+01 angle pdb=" N PRO F 26 " pdb=" CA PRO F 26 " pdb=" CB PRO F 26 " ideal model delta sigma weight residual 103.25 110.15 -6.90 1.05e+00 9.07e-01 4.32e+01 angle pdb=" N PRO J 40 " pdb=" CA PRO J 40 " pdb=" CB PRO J 40 " ideal model delta sigma weight residual 103.00 110.21 -7.21 1.10e+00 8.26e-01 4.29e+01 ... (remaining 38020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 14980 17.69 - 35.39: 1650 35.39 - 53.08: 318 53.08 - 70.77: 37 70.77 - 88.47: 19 Dihedral angle restraints: 17004 sinusoidal: 6339 harmonic: 10665 Sorted by residual: dihedral pdb=" CA ALA B 197 " pdb=" C ALA B 197 " pdb=" N GLU B 198 " pdb=" CA GLU B 198 " ideal model delta harmonic sigma weight residual -180.00 -144.57 -35.43 0 5.00e+00 4.00e-02 5.02e+01 dihedral pdb=" CA LYS B 209 " pdb=" C LYS B 209 " pdb=" N ILE B 210 " pdb=" CA ILE B 210 " ideal model delta harmonic sigma weight residual -180.00 -151.37 -28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA HIS D 125 " pdb=" C HIS D 125 " pdb=" N TYR D 126 " pdb=" CA TYR D 126 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 17001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3240 0.054 - 0.109: 1063 0.109 - 0.163: 185 0.163 - 0.217: 6 0.217 - 0.271: 3 Chirality restraints: 4497 Sorted by residual: chirality pdb=" CA PRO F 24 " pdb=" N PRO F 24 " pdb=" C PRO F 24 " pdb=" CB PRO F 24 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA PRO J 40 " pdb=" N PRO J 40 " pdb=" C PRO J 40 " pdb=" CB PRO J 40 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO F 26 " pdb=" N PRO F 26 " pdb=" C PRO F 26 " pdb=" CB PRO F 26 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 4494 not shown) Planarity restraints: 4909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 395 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO G 396 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 395 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.12e+00 pdb=" N PRO H 396 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO H 396 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 396 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 364 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO H 365 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO H 365 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 365 " 0.024 5.00e-02 4.00e+02 ... (remaining 4906 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 631 2.65 - 3.21: 28296 3.21 - 3.77: 42112 3.77 - 4.34: 57075 4.34 - 4.90: 94056 Nonbonded interactions: 222170 Sorted by model distance: nonbonded pdb=" OG1 THR D 76 " pdb=" OG1 THR D 238 " model vdw 2.082 2.440 nonbonded pdb=" O PRO E 95 " pdb=" NZ LYS E 98 " model vdw 2.084 2.520 nonbonded pdb=" OH TYR F 94 " pdb=" OD1 ASP F 213 " model vdw 2.089 2.440 nonbonded pdb=" OD2 ASP J 62 " pdb=" OG SER J 433 " model vdw 2.096 2.440 nonbonded pdb=" O LYS E 235 " pdb=" OG SER E 238 " model vdw 2.124 2.440 ... (remaining 222165 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' and (resid 1 through 253 or resid 268 through 305)) selection = (chain 'B' and (resid 1 through 90 or (resid 91 and (name N or name CA or name C \ or name O or name CB )) or resid 92 through 305)) } ncs_group { reference = (chain 'C' and (resid 8 through 343 or (resid 344 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 345 through 351)) selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 1 through 11 or resid 25 through 444)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 41 through 170 or (resid 171 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ )) or resid \ 172 through 467)) selection = (chain 'J' and resid 41 through 467) } 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 P 1 5.49 5 S 142 5.16 5 C 17407 2.51 5 N 4827 2.21 5 O 5152 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.440 Check model and map are aligned: 0.430 Process input model: 70.730 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.250 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 0.064 28003 Z= 0.577 Angle : 0.919 18.183 38025 Z= 0.525 Chirality : 0.052 0.271 4497 Planarity : 0.005 0.063 4909 Dihedral : 15.228 88.467 10066 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 16.65 % Favored : 83.13 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.12), residues: 3610 helix: -1.98 (0.12), residues: 1258 sheet: -4.19 (0.19), residues: 442 loop : -3.92 (0.12), residues: 1910 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 426 time to evaluate : 3.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 432 average time/residue: 0.4130 time to fit residues: 278.2420 Evaluate side-chains 317 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 311 time to evaluate : 3.427 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2359 time to fit residues: 7.2978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 0.7980 chunk 273 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 282 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 chunk 210 optimal weight: 0.5980 chunk 327 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 48 ASN A 214 GLN A 244 GLN B 13 GLN B 116 HIS B 213 ASN C 80 ASN C 138 ASN C 158 HIS C 230 ASN D 44 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS D 277 GLN D 280 ASN D 331 ASN E 41 ASN E 190 HIS E 283 ASN F 115 HIS G 265 GLN H 265 GLN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 GLN H 422 GLN ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 HIS J 105 HIS J 160 ASN J 248 HIS J 288 HIS J 359 ASN J 376 ASN J 440 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 28003 Z= 0.237 Angle : 0.642 10.919 38025 Z= 0.326 Chirality : 0.046 0.210 4497 Planarity : 0.005 0.076 4909 Dihedral : 5.436 28.832 3924 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.45 % Favored : 91.44 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.13), residues: 3610 helix: -0.66 (0.14), residues: 1274 sheet: -3.75 (0.20), residues: 452 loop : -3.21 (0.13), residues: 1884 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 393 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 39 residues processed: 436 average time/residue: 0.3585 time to fit residues: 258.5263 Evaluate side-chains 354 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 315 time to evaluate : 3.443 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2536 time to fit residues: 22.8090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 30.0000 chunk 101 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 328 optimal weight: 0.8980 chunk 354 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 325 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 HIS ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 HIS ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 28003 Z= 0.241 Angle : 0.621 10.476 38025 Z= 0.313 Chirality : 0.045 0.173 4497 Planarity : 0.004 0.066 4909 Dihedral : 5.175 27.633 3924 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.67 % Favored : 90.22 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.14), residues: 3610 helix: -0.15 (0.15), residues: 1273 sheet: -3.38 (0.22), residues: 415 loop : -2.96 (0.13), residues: 1922 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 349 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 29 residues processed: 399 average time/residue: 0.3483 time to fit residues: 234.6422 Evaluate side-chains 338 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 309 time to evaluate : 3.761 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2440 time to fit residues: 18.1299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 0.1980 chunk 246 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 220 optimal weight: 0.8980 chunk 329 optimal weight: 0.5980 chunk 348 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 312 optimal weight: 0.0970 chunk 94 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 GLN G 190 ASN G 213 GLN G 411 ASN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 HIS J 288 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 28003 Z= 0.184 Angle : 0.590 10.686 38025 Z= 0.295 Chirality : 0.044 0.209 4497 Planarity : 0.004 0.063 4909 Dihedral : 4.873 25.317 3924 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.37 % Favored : 92.52 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.14), residues: 3610 helix: 0.22 (0.15), residues: 1286 sheet: -2.98 (0.23), residues: 425 loop : -2.72 (0.13), residues: 1899 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 349 time to evaluate : 3.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 29 residues processed: 391 average time/residue: 0.3597 time to fit residues: 237.1892 Evaluate side-chains 334 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 305 time to evaluate : 3.688 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2753 time to fit residues: 20.1913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 259 optimal weight: 0.2980 chunk 143 optimal weight: 0.7980 chunk 297 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 313 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN C 44 GLN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 28003 Z= 0.268 Angle : 0.618 9.464 38025 Z= 0.310 Chirality : 0.045 0.162 4497 Planarity : 0.004 0.065 4909 Dihedral : 4.924 27.014 3924 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.45 % Favored : 90.44 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.14), residues: 3610 helix: 0.34 (0.15), residues: 1286 sheet: -3.04 (0.23), residues: 418 loop : -2.63 (0.14), residues: 1906 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 323 time to evaluate : 3.639 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 32 residues processed: 363 average time/residue: 0.3356 time to fit residues: 209.3823 Evaluate side-chains 342 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 310 time to evaluate : 3.435 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2534 time to fit residues: 19.9339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 0.9980 chunk 314 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 86 optimal weight: 0.0040 chunk 349 optimal weight: 8.9990 chunk 289 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 183 optimal weight: 20.0000 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 288 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 28003 Z= 0.206 Angle : 0.585 9.753 38025 Z= 0.292 Chirality : 0.044 0.187 4497 Planarity : 0.004 0.062 4909 Dihedral : 4.737 25.348 3924 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.19 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.14), residues: 3610 helix: 0.50 (0.15), residues: 1286 sheet: -2.90 (0.23), residues: 452 loop : -2.49 (0.14), residues: 1872 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 340 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 30 residues processed: 378 average time/residue: 0.3504 time to fit residues: 226.2466 Evaluate side-chains 357 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 327 time to evaluate : 3.722 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3042 time to fit residues: 20.9403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 0.4980 chunk 39 optimal weight: 0.0970 chunk 199 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 197 optimal weight: 0.1980 chunk 294 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 347 optimal weight: 0.0170 chunk 217 optimal weight: 2.9990 chunk 212 optimal weight: 0.4980 chunk 160 optimal weight: 2.9990 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 477 GLN ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 28003 Z= 0.159 Angle : 0.567 9.942 38025 Z= 0.282 Chirality : 0.043 0.157 4497 Planarity : 0.004 0.063 4909 Dihedral : 4.491 23.054 3924 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.59 % Favored : 93.30 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.14), residues: 3610 helix: 0.72 (0.15), residues: 1287 sheet: -2.82 (0.22), residues: 485 loop : -2.30 (0.14), residues: 1838 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 365 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 12 residues processed: 394 average time/residue: 0.3560 time to fit residues: 237.2526 Evaluate side-chains 329 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 317 time to evaluate : 3.406 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2475 time to fit residues: 10.2581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 221 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 172 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 273 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 HIS ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 HIS ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 28003 Z= 0.206 Angle : 0.593 9.532 38025 Z= 0.294 Chirality : 0.044 0.244 4497 Planarity : 0.004 0.063 4909 Dihedral : 4.513 23.848 3924 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.48 % Favored : 92.41 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3610 helix: 0.79 (0.15), residues: 1288 sheet: -2.79 (0.22), residues: 476 loop : -2.26 (0.14), residues: 1846 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 331 time to evaluate : 3.417 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 347 average time/residue: 0.3598 time to fit residues: 213.3244 Evaluate side-chains 329 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 314 time to evaluate : 3.565 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2701 time to fit residues: 12.3162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 3.9990 chunk 333 optimal weight: 0.7980 chunk 304 optimal weight: 2.9990 chunk 324 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 306 optimal weight: 0.9990 chunk 323 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 HIS ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 288 HIS ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 28003 Z= 0.258 Angle : 0.619 9.267 38025 Z= 0.309 Chirality : 0.045 0.251 4497 Planarity : 0.004 0.062 4909 Dihedral : 4.672 24.341 3924 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.25 % Favored : 91.63 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3610 helix: 0.73 (0.15), residues: 1291 sheet: -2.88 (0.22), residues: 451 loop : -2.20 (0.14), residues: 1868 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 327 time to evaluate : 3.350 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 339 average time/residue: 0.3631 time to fit residues: 208.9548 Evaluate side-chains 320 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 309 time to evaluate : 3.419 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2735 time to fit residues: 10.2834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 0.0470 chunk 342 optimal weight: 3.9990 chunk 209 optimal weight: 0.5980 chunk 162 optimal weight: 0.9980 chunk 238 optimal weight: 0.6980 chunk 359 optimal weight: 30.0000 chunk 331 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 221 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 ASN ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 288 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 28003 Z= 0.205 Angle : 0.613 14.137 38025 Z= 0.303 Chirality : 0.045 0.256 4497 Planarity : 0.004 0.061 4909 Dihedral : 4.591 24.241 3924 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.12 % Favored : 92.77 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 3610 helix: 0.76 (0.15), residues: 1304 sheet: -2.71 (0.22), residues: 475 loop : -2.11 (0.14), residues: 1831 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 325 time to evaluate : 3.688 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 329 average time/residue: 0.4249 time to fit residues: 238.7764 Evaluate side-chains 316 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 310 time to evaluate : 3.453 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2770 time to fit residues: 8.1851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 1.9990 chunk 305 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 264 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 288 HIS ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.140087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.122582 restraints weight = 41328.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122079 restraints weight = 58623.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.123119 restraints weight = 48277.017| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 28003 Z= 0.251 Angle : 0.625 9.343 38025 Z= 0.312 Chirality : 0.046 0.344 4497 Planarity : 0.004 0.062 4909 Dihedral : 4.676 24.476 3924 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.17 % Favored : 91.72 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.14), residues: 3610 helix: 0.68 (0.15), residues: 1312 sheet: -2.77 (0.22), residues: 482 loop : -2.12 (0.14), residues: 1816 =============================================================================== Job complete usr+sys time: 5088.79 seconds wall clock time: 94 minutes 38.38 seconds (5678.38 seconds total)