Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 21:48:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfo_27409/04_2023/8dfo_27409.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfo_27409/04_2023/8dfo_27409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfo_27409/04_2023/8dfo_27409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfo_27409/04_2023/8dfo_27409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfo_27409/04_2023/8dfo_27409.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfo_27409/04_2023/8dfo_27409.pdb" } resolution = 3.1 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= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 45 5.49 5 S 135 5.16 5 C 14839 2.51 5 N 4259 2.21 5 O 4583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 31": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ARG 94": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C ARG 242": "NH1" <-> "NH2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "D ARG 7": "NH1" <-> "NH2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 142": "NH1" <-> "NH2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ARG 268": "NH1" <-> "NH2" Residue "E ARG 7": "NH1" <-> "NH2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "E ARG 142": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 173": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 222": "NH1" <-> "NH2" Residue "E ARG 226": "NH1" <-> "NH2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 242": "NH1" <-> "NH2" Residue "E ARG 259": "NH1" <-> "NH2" Residue "E ARG 268": "NH1" <-> "NH2" Residue "F ARG 7": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F ARG 81": "NH1" <-> "NH2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "F ARG 117": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F ARG 142": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ARG 173": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 222": "NH1" <-> "NH2" Residue "F ARG 226": "NH1" <-> "NH2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F ARG 242": "NH1" <-> "NH2" Residue "F ARG 259": "NH1" <-> "NH2" Residue "F ARG 268": "NH1" <-> "NH2" Residue "G ARG 7": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ARG 52": "NH1" <-> "NH2" Residue "G ARG 64": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 104": "NH1" <-> "NH2" Residue "G ARG 117": "NH1" <-> "NH2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G ARG 142": "NH1" <-> "NH2" Residue "G ARG 156": "NH1" <-> "NH2" Residue "G ARG 173": "NH1" <-> "NH2" Residue "G ARG 177": "NH1" <-> "NH2" Residue "G ARG 222": "NH1" <-> "NH2" Residue "G ARG 226": "NH1" <-> "NH2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G ARG 242": "NH1" <-> "NH2" Residue "G ARG 259": "NH1" <-> "NH2" Residue "G ARG 268": "NH1" <-> "NH2" Residue "H ARG 7": "NH1" <-> "NH2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 32": "NH1" <-> "NH2" Residue "H ARG 49": "NH1" <-> "NH2" Residue "H ARG 52": "NH1" <-> "NH2" Residue "H ARG 64": "NH1" <-> "NH2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H ARG 104": "NH1" <-> "NH2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "H ARG 133": "NH1" <-> "NH2" Residue "H ARG 142": "NH1" <-> "NH2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H ARG 173": "NH1" <-> "NH2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "H ARG 222": "NH1" <-> "NH2" Residue "H ARG 226": "NH1" <-> "NH2" Residue "H ARG 232": "NH1" <-> "NH2" Residue "H ARG 242": "NH1" <-> "NH2" Residue "H ARG 259": "NH1" <-> "NH2" Residue "H ARG 268": "NH1" <-> "NH2" Residue "I ARG 12": "NH1" <-> "NH2" Residue "I ARG 190": "NH1" <-> "NH2" Residue "I ARG 205": "NH1" <-> "NH2" Residue "I ARG 209": "NH1" <-> "NH2" Residue "I ARG 259": "NH1" <-> "NH2" Residue "I ARG 275": "NH1" <-> "NH2" Residue "I ARG 325": "NH1" <-> "NH2" Residue "I ARG 334": "NH1" <-> "NH2" Residue "I ARG 338": "NH1" <-> "NH2" Residue "I ARG 351": "NH1" <-> "NH2" Residue "I ARG 363": "NH1" <-> "NH2" Residue "I ARG 367": "NH1" <-> "NH2" Residue "I ARG 383": "NH1" <-> "NH2" Residue "I ARG 386": "NH1" <-> "NH2" Residue "I ARG 408": "NH1" <-> "NH2" Residue "I ARG 429": "NH1" <-> "NH2" Residue "I ARG 448": "NH1" <-> "NH2" Residue "I ARG 450": "NH1" <-> "NH2" Residue "I ARG 455": "NH1" <-> "NH2" Residue "I ARG 461": "NH1" <-> "NH2" Residue "I ARG 463": "NH1" <-> "NH2" Residue "I ARG 471": "NH1" <-> "NH2" Residue "I ARG 481": "NH1" <-> "NH2" Residue "I ARG 483": "NH1" <-> "NH2" Residue "I ARG 495": "NH1" <-> "NH2" Residue "I ARG 498": "NH1" <-> "NH2" Residue "I ARG 504": "NH1" <-> "NH2" Residue "I ARG 527": "NH1" <-> "NH2" Residue "I ARG 555": "NH1" <-> "NH2" Residue "I ARG 560": "NH1" <-> "NH2" Residue "I ARG 601": "NH1" <-> "NH2" Residue "J ARG 7": "NH1" <-> "NH2" Residue "J ARG 10": "NH1" <-> "NH2" Residue "J ARG 16": "NH1" <-> "NH2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 72": "NH1" <-> "NH2" Residue "J ARG 113": "NH1" <-> "NH2" Residue "K ARG 7": "NH1" <-> "NH2" Residue "K ARG 10": "NH1" <-> "NH2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ARG 39": "NH1" <-> "NH2" Residue "K ARG 67": "NH1" <-> "NH2" Residue "K ARG 72": "NH1" <-> "NH2" Residue "K ARG 113": "NH1" <-> "NH2" Residue "M ARG 14": "NH1" <-> "NH2" Residue "M ARG 53": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 23861 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1774 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "B" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2112 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 2 Chain: "C" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "D" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "E" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "F" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "G" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "H" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "I" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3261 Classifications: {'peptide': 415} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 388} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "K" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain breaks: 1 Chain: "L" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 960 Classifications: {'RNA': 45} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 8, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna2p': 17, 'rna3p': 27} Chain: "M" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 466 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Time building chain proxies: 11.87, per 1000 atoms: 0.50 Number of scatterers: 23861 At special positions: 0 Unit cell: (119.38, 117.5, 202.1, 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 135 16.00 P 45 15.00 O 4583 8.00 N 4259 7.00 C 14839 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: 10.27 Conformation dependent library (CDL) restraints added in 3.2 seconds 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5458 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 36 sheets defined 38.0% alpha, 23.7% beta 0 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 6.46 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.784A pdb=" N LYS A 28 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 Processing helix chain 'A' and resid 88 through 93 removed outlier: 4.167A pdb=" N ASP A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'B' and resid 43 through 60 Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.883A pdb=" N ASN B 112 " --> pdb=" O TRP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 119 Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 193 through 199 removed outlier: 3.561A pdb=" N LYS B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 217 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'C' and resid 43 through 60 removed outlier: 3.545A pdb=" N LEU C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 removed outlier: 3.548A pdb=" N ALA C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 113 Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.567A pdb=" N LYS C 199 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 217 through 221 removed outlier: 4.320A pdb=" N HIS C 220 " --> pdb=" O MET C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'D' and resid 43 through 60 removed outlier: 3.628A pdb=" N LEU D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 86 removed outlier: 3.606A pdb=" N THR D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 113 Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.539A pdb=" N LYS D 199 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.785A pdb=" N SER D 263 " --> pdb=" O ALA D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'E' and resid 43 through 60 removed outlier: 3.540A pdb=" N LEU E 47 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 98 through 113 Processing helix chain 'E' and resid 113 through 120 Processing helix chain 'E' and resid 193 through 201 removed outlier: 3.930A pdb=" N LYS E 199 " --> pdb=" O PRO E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 247 through 253 Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'F' and resid 43 through 60 removed outlier: 3.551A pdb=" N LEU F 47 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 98 through 113 Processing helix chain 'F' and resid 113 through 120 Processing helix chain 'F' and resid 193 through 201 removed outlier: 3.595A pdb=" N LYS F 199 " --> pdb=" O PRO F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 Processing helix chain 'F' and resid 247 through 253 Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'G' and resid 24 through 28 removed outlier: 3.916A pdb=" N GLY G 28 " --> pdb=" O PRO G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 60 removed outlier: 3.645A pdb=" N LEU G 47 " --> pdb=" O THR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 98 through 113 Processing helix chain 'G' and resid 113 through 120 Processing helix chain 'G' and resid 193 through 201 removed outlier: 3.560A pdb=" N LYS G 199 " --> pdb=" O PRO G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 216 Processing helix chain 'G' and resid 217 through 221 removed outlier: 4.163A pdb=" N HIS G 220 " --> pdb=" O MET G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 255 removed outlier: 3.607A pdb=" N LEU G 254 " --> pdb=" O LYS G 250 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL G 255 " --> pdb=" O LEU G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'H' and resid 24 through 28 removed outlier: 3.787A pdb=" N GLY H 28 " --> pdb=" O PRO H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 removed outlier: 3.763A pdb=" N LEU H 47 " --> pdb=" O THR H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 87 Processing helix chain 'H' and resid 98 through 113 Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'H' and resid 193 through 201 removed outlier: 4.177A pdb=" N LYS H 199 " --> pdb=" O PRO H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 Processing helix chain 'H' and resid 247 through 255 removed outlier: 3.583A pdb=" N ASP H 253 " --> pdb=" O HIS H 249 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL H 255 " --> pdb=" O LEU H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 271 No H-bonds generated for 'chain 'H' and resid 269 through 271' Processing helix chain 'I' and resid 4 through 14 Processing helix chain 'I' and resid 239 through 255 removed outlier: 3.568A pdb=" N VAL I 247 " --> pdb=" O ALA I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 287 removed outlier: 4.343A pdb=" N ALA I 284 " --> pdb=" O GLU I 280 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY I 285 " --> pdb=" O ASP I 281 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE I 287 " --> pdb=" O PHE I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 335 Processing helix chain 'I' and resid 338 through 342 Processing helix chain 'I' and resid 373 through 389 Processing helix chain 'I' and resid 402 through 409 Processing helix chain 'I' and resid 420 through 427 Processing helix chain 'I' and resid 430 through 434 Processing helix chain 'I' and resid 440 through 452 Processing helix chain 'I' and resid 455 through 459 removed outlier: 4.018A pdb=" N ASP I 458 " --> pdb=" O ARG I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 468 through 482 Processing helix chain 'I' and resid 497 through 517 Processing helix chain 'I' and resid 523 through 528 removed outlier: 3.758A pdb=" N ARG I 527 " --> pdb=" O THR I 523 " (cutoff:3.500A) Processing helix chain 'I' and resid 528 through 535 Processing helix chain 'I' and resid 535 through 557 removed outlier: 3.885A pdb=" N VAL I 539 " --> pdb=" O ASN I 535 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N HIS I 541 " --> pdb=" O GLY I 537 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N MET I 542 " --> pdb=" O GLN I 538 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS I 556 " --> pdb=" O ALA I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 564 through 576 removed outlier: 3.825A pdb=" N GLU I 568 " --> pdb=" O ALA I 564 " (cutoff:3.500A) Processing helix chain 'I' and resid 586 through 603 Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 35 through 40 Processing helix chain 'J' and resid 40 through 47 Processing helix chain 'J' and resid 47 through 69 removed outlier: 3.655A pdb=" N VAL J 51 " --> pdb=" O ASN J 47 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N HIS J 53 " --> pdb=" O GLY J 49 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N MET J 54 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP J 69 " --> pdb=" O LYS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.843A pdb=" N ASN J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 118 Processing helix chain 'K' and resid 9 through 29 Processing helix chain 'K' and resid 35 through 47 removed outlier: 3.516A pdb=" N ARG K 39 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA K 42 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 68 removed outlier: 3.708A pdb=" N VAL K 51 " --> pdb=" O ASN K 47 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS K 53 " --> pdb=" O GLY K 49 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET K 54 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN K 61 " --> pdb=" O LYS K 57 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 73 No H-bonds generated for 'chain 'K' and resid 73 through 73' Processing helix chain 'K' and resid 77 through 90 Processing helix chain 'K' and resid 98 through 118 Processing helix chain 'M' and resid 6 through 8 No H-bonds generated for 'chain 'M' and resid 6 through 8' Processing helix chain 'M' and resid 9 through 18 Processing helix chain 'M' and resid 42 through 56 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.769A pdb=" N ARG A 31 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N LEU A 115 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG A 116 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR A 19 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 78 removed outlier: 3.552A pdb=" N ARG A 75 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP A 119 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL A 64 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 121 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 62 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU A 123 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 196 removed outlier: 5.697A pdb=" N ALA A 208 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR A 190 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE A 206 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU A 192 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU A 204 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP A 194 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR A 202 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.867A pdb=" N THR B 174 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 136 through 138 removed outlier: 3.506A pdb=" N GLY B 184 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP B 15 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N SER B 231 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLU B 17 " --> pdb=" O MET B 229 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N MET B 229 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 234 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AA8, first strand: chain 'B' and resid 255 through 259 Processing sheet with id=AA9, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 19 removed outlier: 6.921A pdb=" N GLU C 17 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR C 183 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 121 through 124 removed outlier: 4.515A pdb=" N GLY C 130 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 255 through 259 Processing sheet with id=AB5, first strand: chain 'D' and resid 41 through 42 Processing sheet with id=AB6, first strand: chain 'D' and resid 136 through 138 removed outlier: 6.753A pdb=" N TYR D 183 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU D 17 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU D 185 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP D 15 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL D 187 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU D 13 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N HIS D 189 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 11 " --> pdb=" O HIS D 189 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE D 191 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU D 9 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASP D 15 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER D 231 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLU D 17 " --> pdb=" O MET D 229 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N MET D 229 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU D 234 " --> pdb=" O MET D 289 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AB8, first strand: chain 'D' and resid 255 through 258 Processing sheet with id=AB9, first strand: chain 'E' and resid 41 through 42 Processing sheet with id=AC1, first strand: chain 'E' and resid 136 through 138 removed outlier: 6.880A pdb=" N ASP E 15 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N SER E 231 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU E 234 " --> pdb=" O MET E 289 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 121 through 122 Processing sheet with id=AC3, first strand: chain 'E' and resid 255 through 259 Processing sheet with id=AC4, first strand: chain 'F' and resid 41 through 42 removed outlier: 3.643A pdb=" N THR F 174 " --> pdb=" O ARG F 156 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 136 through 138 removed outlier: 3.832A pdb=" N ARG F 7 " --> pdb=" O HIS F 239 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP F 15 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER F 231 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLU F 17 " --> pdb=" O MET F 229 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N MET F 229 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 121 through 123 removed outlier: 3.557A pdb=" N GLY F 130 " --> pdb=" O MET F 123 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 255 through 259 Processing sheet with id=AC8, first strand: chain 'G' and resid 39 through 42 removed outlier: 5.134A pdb=" N GLY G 40 " --> pdb=" O SER G 143 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU G 185 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR G 183 " --> pdb=" O PRO G 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 136 through 138 removed outlier: 5.939A pdb=" N ASP G 15 " --> pdb=" O SER G 231 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER G 231 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLU G 17 " --> pdb=" O MET G 229 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N MET G 229 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 121 through 124 removed outlier: 3.737A pdb=" N GLY G 130 " --> pdb=" O MET G 123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 41 through 42 Processing sheet with id=AD3, first strand: chain 'H' and resid 136 through 138 removed outlier: 3.585A pdb=" N LYS H 233 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP H 15 " --> pdb=" O SER H 231 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N SER H 231 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLU H 17 " --> pdb=" O MET H 229 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N MET H 229 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 121 through 123 Processing sheet with id=AD5, first strand: chain 'H' and resid 257 through 259 Processing sheet with id=AD6, first strand: chain 'I' and resid 181 through 182 Processing sheet with id=AD7, first strand: chain 'I' and resid 201 through 202 Processing sheet with id=AD8, first strand: chain 'I' and resid 262 through 264 removed outlier: 6.630A pdb=" N VAL I 354 " --> pdb=" O TRP I 369 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP I 369 " --> pdb=" O VAL I 354 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY I 356 " --> pdb=" O ARG I 367 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 22 through 24 1005 hydrogen bonds defined for protein. 2841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 11.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.43: 10772 1.43 - 1.82: 13669 1.82 - 2.21: 0 2.21 - 2.61: 0 2.61 - 3.00: 2 Bond restraints: 24443 Sorted by residual: bond pdb=" C LYS J 73 " pdb=" N ALA J 76 " ideal model delta sigma weight residual 1.332 2.998 -1.665 1.40e-02 5.10e+03 1.41e+04 bond pdb=" CB PRO H 92 " pdb=" CG PRO H 92 " ideal model delta sigma weight residual 1.492 2.673 -1.181 5.00e-02 4.00e+02 5.58e+02 bond pdb=" CG PRO H 92 " pdb=" CD PRO H 92 " ideal model delta sigma weight residual 1.503 1.038 0.465 3.40e-02 8.65e+02 1.87e+02 bond pdb=" CE1 HIS C 249 " pdb=" NE2 HIS C 249 " ideal model delta sigma weight residual 1.321 1.231 0.090 1.00e-02 1.00e+04 8.02e+01 bond pdb=" CE1 HIS C 54 " pdb=" NE2 HIS C 54 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.90e+01 ... (remaining 24438 not shown) Histogram of bond angle deviations from ideal: 0.05 - 29.66: 1 29.66 - 59.27: 1 59.27 - 88.88: 2 88.88 - 118.48: 19130 118.48 - 148.09: 14136 Bond angle restraints: 33270 Sorted by residual: angle pdb=" O LYS J 73 " pdb=" C LYS J 73 " pdb=" N ALA J 76 " ideal model delta sigma weight residual 122.59 37.08 85.51 1.33e+00 5.65e-01 4.13e+03 angle pdb=" CB PRO H 92 " pdb=" CG PRO H 92 " pdb=" CD PRO H 92 " ideal model delta sigma weight residual 106.10 0.05 106.05 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA LYS J 73 " pdb=" C LYS J 73 " pdb=" N ALA J 76 " ideal model delta sigma weight residual 116.84 84.80 32.04 1.71e+00 3.42e-01 3.51e+02 angle pdb=" CA PRO H 92 " pdb=" N PRO H 92 " pdb=" CD PRO H 92 " ideal model delta sigma weight residual 112.00 89.53 22.47 1.40e+00 5.10e-01 2.58e+02 angle pdb=" N PRO H 92 " pdb=" CA PRO H 92 " pdb=" CB PRO H 92 " ideal model delta sigma weight residual 103.19 92.31 10.88 1.00e+00 1.00e+00 1.18e+02 ... (remaining 33265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 14272 35.53 - 71.07: 454 71.07 - 106.60: 37 106.60 - 142.14: 7 142.14 - 177.67: 14 Dihedral angle restraints: 14784 sinusoidal: 6355 harmonic: 8429 Sorted by residual: dihedral pdb=" C5' U L 5 " pdb=" C4' U L 5 " pdb=" C3' U L 5 " pdb=" O3' U L 5 " ideal model delta sinusoidal sigma weight residual 147.00 74.29 72.71 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C4' C L 18 " pdb=" C3' C L 18 " pdb=" C2' C L 18 " pdb=" C1' C L 18 " ideal model delta sinusoidal sigma weight residual -35.00 36.08 -71.08 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' G L 31 " pdb=" C3' G L 31 " pdb=" C2' G L 31 " pdb=" C1' G L 31 " ideal model delta sinusoidal sigma weight residual -35.00 35.81 -70.81 1 8.00e+00 1.56e-02 1.01e+02 ... (remaining 14781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 3302 0.148 - 0.296: 73 0.296 - 0.444: 84 0.444 - 0.592: 171 0.592 - 0.740: 64 Chirality restraints: 3694 Sorted by residual: chirality pdb=" CG LEU I 364 " pdb=" CB LEU I 364 " pdb=" CD1 LEU I 364 " pdb=" CD2 LEU I 364 " both_signs ideal model delta sigma weight residual False -2.59 -1.85 -0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CG LEU C 12 " pdb=" CB LEU C 12 " pdb=" CD1 LEU C 12 " pdb=" CD2 LEU C 12 " both_signs ideal model delta sigma weight residual False -2.59 -1.85 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CB VAL C 11 " pdb=" CA VAL C 11 " pdb=" CG1 VAL C 11 " pdb=" CG2 VAL C 11 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.33e+01 ... (remaining 3691 not shown) Planarity restraints: 4206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U L 6 " -0.179 2.00e-02 2.50e+03 8.31e-02 1.55e+02 pdb=" N1 U L 6 " 0.078 2.00e-02 2.50e+03 pdb=" C2 U L 6 " 0.033 2.00e-02 2.50e+03 pdb=" O2 U L 6 " 0.046 2.00e-02 2.50e+03 pdb=" N3 U L 6 " 0.009 2.00e-02 2.50e+03 pdb=" C4 U L 6 " -0.016 2.00e-02 2.50e+03 pdb=" O4 U L 6 " -0.102 2.00e-02 2.50e+03 pdb=" C5 U L 6 " 0.039 2.00e-02 2.50e+03 pdb=" C6 U L 6 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G L 7 " 0.118 2.00e-02 2.50e+03 5.10e-02 7.82e+01 pdb=" N9 G L 7 " -0.015 2.00e-02 2.50e+03 pdb=" C8 G L 7 " -0.064 2.00e-02 2.50e+03 pdb=" N7 G L 7 " -0.050 2.00e-02 2.50e+03 pdb=" C5 G L 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G L 7 " 0.029 2.00e-02 2.50e+03 pdb=" O6 G L 7 " 0.045 2.00e-02 2.50e+03 pdb=" N1 G L 7 " 0.052 2.00e-02 2.50e+03 pdb=" C2 G L 7 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G L 7 " -0.051 2.00e-02 2.50e+03 pdb=" N3 G L 7 " -0.044 2.00e-02 2.50e+03 pdb=" C4 G L 7 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 8 " -0.077 2.00e-02 2.50e+03 3.95e-02 3.13e+01 pdb=" CG TYR C 8 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR C 8 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR C 8 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR C 8 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR C 8 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 8 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 8 " -0.049 2.00e-02 2.50e+03 ... (remaining 4203 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 75 2.36 - 2.99: 13234 2.99 - 3.63: 34940 3.63 - 4.26: 55886 4.26 - 4.90: 95992 Nonbonded interactions: 200127 Sorted by model distance: nonbonded pdb=" O2' G L 12 " pdb=" O5' C L 13 " model vdw 1.724 2.440 nonbonded pdb=" O2' A L 15 " pdb=" O5' U L 16 " model vdw 1.742 2.440 nonbonded pdb=" O2' U L 42 " pdb=" O5' C L 43 " model vdw 1.797 2.440 nonbonded pdb=" O2' G L 33 " pdb=" O5' C L 34 " model vdw 1.802 2.440 nonbonded pdb=" O2' C L 34 " pdb=" OP1 G L 35 " model vdw 1.839 2.440 ... (remaining 200122 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 'B' selection = (chain 'C' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'D' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'E' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'F' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'G' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'H' and (resid 1 through 84 or resid 101 through 290)) } ncs_group { reference = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 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: 3.530 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: 18.010 Check model and map are aligned: 0.350 Set scattering table: 0.190 Process input model: 65.020 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0735 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 : 0.022 1.665 24443 Z= 1.420 Angle : 1.638 106.046 33270 Z= 0.977 Chirality : 0.163 0.740 3694 Planarity : 0.006 0.100 4206 Dihedral : 17.807 177.673 9326 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.76 % Favored : 95.21 % Rotamer Outliers : 0.57 % Cbeta Deviations : 3.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 2860 helix: 0.78 (0.17), residues: 916 sheet: -0.09 (0.22), residues: 559 loop : -1.10 (0.16), residues: 1385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 335 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 347 average time/residue: 0.4260 time to fit residues: 221.0620 Evaluate side-chains 219 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 217 time to evaluate : 2.647 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2122 time to fit residues: 4.6947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 147 optimal weight: 0.4980 chunk 117 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 168 optimal weight: 20.0000 chunk 262 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 157 GLN C 70 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN E 220 HIS ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS H 216 ASN I 198 HIS ** I 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN J 111 HIS J 112 GLN ** M 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2081 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.151 24443 Z= 0.354 Angle : 0.930 14.107 33270 Z= 0.483 Chirality : 0.053 0.415 3694 Planarity : 0.008 0.075 4206 Dihedral : 13.041 156.114 3719 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.26 % Favored : 95.63 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 2862 helix: 0.38 (0.16), residues: 945 sheet: 0.02 (0.22), residues: 508 loop : -1.02 (0.16), residues: 1409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 270 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 30 residues processed: 330 average time/residue: 0.3997 time to fit residues: 206.8608 Evaluate side-chains 248 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 218 time to evaluate : 2.734 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3044 time to fit residues: 21.4267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 145 optimal weight: 0.0970 chunk 81 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 262 optimal weight: 2.9990 chunk 284 optimal weight: 0.0000 chunk 234 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 210 optimal weight: 0.2980 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN D 189 HIS E 216 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN I 222 ASN I 327 HIS J 112 GLN ** M 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1977 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 24443 Z= 0.163 Angle : 0.627 11.807 33270 Z= 0.325 Chirality : 0.045 0.262 3694 Planarity : 0.004 0.054 4206 Dihedral : 12.323 173.922 3719 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.82 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 2862 helix: 1.32 (0.17), residues: 959 sheet: 0.27 (0.21), residues: 552 loop : -0.66 (0.17), residues: 1351 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 223 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 12 residues processed: 251 average time/residue: 0.3747 time to fit residues: 149.1039 Evaluate side-chains 215 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 203 time to evaluate : 2.576 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2387 time to fit residues: 9.2218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 259 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 29 optimal weight: 0.0170 chunk 125 optimal weight: 0.5980 chunk 176 optimal weight: 0.6980 chunk 263 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 250 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 HIS E 245 ASN F 39 HIS ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 221 ASN ** I 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 546 ASN J 102 GLN ** M 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2165 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 24443 Z= 0.172 Angle : 0.622 11.662 33270 Z= 0.320 Chirality : 0.045 0.280 3694 Planarity : 0.004 0.059 4206 Dihedral : 11.957 176.583 3719 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.12 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2862 helix: 1.57 (0.17), residues: 960 sheet: 0.39 (0.21), residues: 562 loop : -0.68 (0.17), residues: 1340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 235 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 13 residues processed: 260 average time/residue: 0.3642 time to fit residues: 150.8097 Evaluate side-chains 223 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 210 time to evaluate : 2.687 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2361 time to fit residues: 9.4863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 232 optimal weight: 10.0000 chunk 158 optimal weight: 0.0370 chunk 4 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 250 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 76 ASN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN C 150 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 HIS G 179 HIS G 249 HIS H 112 ASN I 258 ASN J 112 GLN K 102 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3193 moved from start: 0.9429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.127 24443 Z= 0.384 Angle : 0.955 15.413 33270 Z= 0.505 Chirality : 0.056 0.332 3694 Planarity : 0.007 0.076 4206 Dihedral : 12.794 173.704 3719 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 25.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.39 % Favored : 93.54 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 2862 helix: -0.11 (0.16), residues: 953 sheet: -0.31 (0.23), residues: 491 loop : -1.28 (0.16), residues: 1418 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 251 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 38 residues processed: 319 average time/residue: 0.3417 time to fit residues: 174.8274 Evaluate side-chains 256 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 218 time to evaluate : 2.504 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2383 time to fit residues: 20.4527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 93 optimal weight: 7.9990 chunk 251 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 164 optimal weight: 0.0070 chunk 68 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN C 70 GLN D 239 HIS F 29 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN H 70 GLN H 216 ASN I 183 GLN ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3101 moved from start: 0.9620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 24443 Z= 0.205 Angle : 0.693 14.133 33270 Z= 0.356 Chirality : 0.046 0.276 3694 Planarity : 0.005 0.058 4206 Dihedral : 12.172 178.110 3719 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.70 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 2862 helix: 0.46 (0.16), residues: 961 sheet: -0.51 (0.22), residues: 519 loop : -1.07 (0.16), residues: 1382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 243 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 263 average time/residue: 0.3619 time to fit residues: 154.5526 Evaluate side-chains 234 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 220 time to evaluate : 2.755 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2938 time to fit residues: 11.1054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 269 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 159 optimal weight: 0.0040 chunk 204 optimal weight: 8.9990 chunk 158 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 278 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 HIS ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 535 ASN ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3157 moved from start: 1.0054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 24443 Z= 0.188 Angle : 0.652 13.025 33270 Z= 0.333 Chirality : 0.045 0.221 3694 Planarity : 0.005 0.056 4206 Dihedral : 11.774 179.894 3719 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.00 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 2862 helix: 0.70 (0.16), residues: 962 sheet: 0.00 (0.23), residues: 508 loop : -1.05 (0.16), residues: 1392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 240 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 252 average time/residue: 0.3788 time to fit residues: 154.0616 Evaluate side-chains 224 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 214 time to evaluate : 2.948 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2346 time to fit residues: 8.2999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 177 optimal weight: 0.0060 chunk 189 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 218 optimal weight: 0.0010 overall best weight: 1.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 HIS ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3319 moved from start: 1.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 24443 Z= 0.212 Angle : 0.681 13.646 33270 Z= 0.350 Chirality : 0.046 0.262 3694 Planarity : 0.005 0.060 4206 Dihedral : 11.634 176.794 3719 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.86 % Favored : 95.11 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 2862 helix: 0.61 (0.16), residues: 967 sheet: -0.16 (0.22), residues: 515 loop : -1.12 (0.16), residues: 1380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 246 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 262 average time/residue: 0.3791 time to fit residues: 157.0235 Evaluate side-chains 228 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 222 time to evaluate : 2.617 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3913 time to fit residues: 7.3778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 253 optimal weight: 0.0870 chunk 266 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 259 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 203 optimal weight: 0.0970 chunk 79 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3283 moved from start: 1.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 24443 Z= 0.171 Angle : 0.634 13.344 33270 Z= 0.321 Chirality : 0.044 0.212 3694 Planarity : 0.005 0.092 4206 Dihedral : 11.440 178.924 3719 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.42 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 2862 helix: 0.81 (0.16), residues: 966 sheet: -0.09 (0.22), residues: 527 loop : -1.09 (0.17), residues: 1369 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 228 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 234 average time/residue: 0.3673 time to fit residues: 138.6264 Evaluate side-chains 220 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 214 time to evaluate : 2.644 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2188 time to fit residues: 6.4615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 20.0000 chunk 274 optimal weight: 0.7980 chunk 167 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 190 optimal weight: 10.0000 chunk 287 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3630 moved from start: 1.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 24443 Z= 0.262 Angle : 0.759 15.171 33270 Z= 0.391 Chirality : 0.049 0.278 3694 Planarity : 0.006 0.069 4206 Dihedral : 11.761 175.309 3719 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.29 % Favored : 93.68 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 2862 helix: 0.22 (0.16), residues: 964 sheet: -0.52 (0.23), residues: 505 loop : -1.29 (0.16), residues: 1393 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 237 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 245 average time/residue: 0.3630 time to fit residues: 145.0909 Evaluate side-chains 214 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 209 time to evaluate : 2.670 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2550 time to fit residues: 6.1656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 182 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 229 optimal weight: 0.9980 chunk 96 optimal weight: 0.3980 chunk 235 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5179 r_free = 0.5179 target = 0.292710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.273898 restraints weight = 41284.673| |-----------------------------------------------------------------------------| r_work (start): 0.5023 rms_B_bonded: 2.37 r_work: 0.4961 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3842 moved from start: 1.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 24443 Z= 0.179 Angle : 0.655 13.898 33270 Z= 0.332 Chirality : 0.045 0.206 3694 Planarity : 0.005 0.067 4206 Dihedral : 11.443 177.623 3719 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.74 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 2862 helix: 0.58 (0.16), residues: 969 sheet: -0.43 (0.22), residues: 527 loop : -1.22 (0.16), residues: 1366 =============================================================================== Job complete usr+sys time: 5031.58 seconds wall clock time: 92 minutes 17.82 seconds (5537.82 seconds total)