Starting phenix.real_space_refine on Tue Mar 19 09:54:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfo_27409/03_2024/8dfo_27409.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfo_27409/03_2024/8dfo_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_27409/03_2024/8dfo_27409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfo_27409/03_2024/8dfo_27409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfo_27409/03_2024/8dfo_27409.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfo_27409/03_2024/8dfo_27409.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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-dev-5265/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: 12.96, per 1000 atoms: 0.54 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: 9.97 Conformation dependent library (CDL) restraints added in 4.3 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: 7.65 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: 7.79 Time building geometry restraints manager: 10.80 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: 14362 35.53 - 71.07: 523 71.07 - 106.60: 50 106.60 - 142.14: 7 142.14 - 177.67: 14 Dihedral angle restraints: 14956 sinusoidal: 6527 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 14953 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: 4.940 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: 16.680 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 68.380 Find NCS groups from input model: 1.340 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.770 ------------------------------------------------------------------------------- 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 : 18.530 177.673 9498 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 % Allowed : 11.72 % Favored : 87.71 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 211 HIS 0.017 0.001 HIS I 198 PHE 0.054 0.003 PHE I 225 TYR 0.077 0.003 TYR C 8 ARG 0.008 0.000 ARG I 363 *********************** 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 : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 MET cc_start: 0.2011 (tpp) cc_final: 0.1500 (ptt) REVERT: D 183 TYR cc_start: 0.1513 (t80) cc_final: 0.0787 (t80) REVERT: E 138 MET cc_start: 0.2902 (mtt) cc_final: 0.0628 (mpp) REVERT: G 175 MET cc_start: 0.5701 (tmm) cc_final: 0.5314 (tmm) REVERT: H 251 LEU cc_start: -0.0135 (mt) cc_final: -0.0390 (mt) REVERT: I 343 MET cc_start: -0.2998 (mtp) cc_final: -0.4121 (tpt) REVERT: I 526 ASP cc_start: 0.2245 (m-30) cc_final: 0.2024 (m-30) REVERT: K 78 HIS cc_start: 0.4984 (t70) cc_final: 0.4741 (t-170) REVERT: M 1 MET cc_start: 0.3480 (mtt) cc_final: 0.2897 (ttp) outliers start: 14 outliers final: 2 residues processed: 347 average time/residue: 0.4091 time to fit residues: 213.1003 Evaluate side-chains 221 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain I residue 364 LEU 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: 5.9990 chunk 226 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 168 optimal weight: 20.0000 chunk 262 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 E 220 HIS E 245 ASN ** 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** J 33 ASN J 111 HIS J 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1871 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.211 24443 Z= 0.310 Angle : 0.833 14.139 33270 Z= 0.436 Chirality : 0.050 0.426 3694 Planarity : 0.006 0.066 4206 Dihedral : 15.460 157.556 3894 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 2.99 % Allowed : 12.99 % Favored : 84.02 % 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: -0.24 (0.15), residues: 2862 helix: 0.78 (0.16), residues: 947 sheet: 0.15 (0.22), residues: 515 loop : -0.90 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP M 40 HIS 0.015 0.002 HIS E 39 PHE 0.032 0.003 PHE C 210 TYR 0.027 0.003 TYR J 12 ARG 0.009 0.001 ARG G 49 *********************** 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 338 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 265 time to evaluate : 2.365 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: A 11 ILE cc_start: 0.7129 (mt) cc_final: 0.6916 (mt) REVERT: A 37 MET cc_start: 0.6438 (ttt) cc_final: 0.6188 (ttt) REVERT: C 30 MET cc_start: 0.0084 (mtp) cc_final: -0.0965 (mtp) REVERT: C 123 MET cc_start: -0.1293 (ptp) cc_final: -0.3217 (mtm) REVERT: C 138 MET cc_start: 0.3516 (ppp) cc_final: 0.0133 (mtm) REVERT: E 138 MET cc_start: 0.3356 (mtt) cc_final: 0.1825 (mpp) REVERT: F 1 MET cc_start: -0.1409 (ptm) cc_final: -0.2308 (mtp) REVERT: G 138 MET cc_start: -0.2254 (ptp) cc_final: -0.3263 (mtm) REVERT: G 272 ASP cc_start: 0.5395 (m-30) cc_final: 0.4968 (t0) REVERT: I 343 MET cc_start: -0.3021 (mtp) cc_final: -0.4363 (tpt) REVERT: I 346 MET cc_start: -0.1477 (OUTLIER) cc_final: -0.2213 (mmm) REVERT: I 514 GLU cc_start: 0.1317 (pt0) cc_final: 0.0847 (tt0) REVERT: J 82 MET cc_start: 0.0929 (mtm) cc_final: -0.0050 (tmm) REVERT: K 97 MET cc_start: -0.1175 (OUTLIER) cc_final: -0.2028 (mpp) REVERT: M 51 GLU cc_start: 0.3693 (OUTLIER) cc_final: 0.3456 (mp0) outliers start: 73 outliers final: 29 residues processed: 316 average time/residue: 0.3544 time to fit residues: 177.3005 Evaluate side-chains 255 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 223 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 268 THR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 578 ILE Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 145 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 218 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 262 optimal weight: 4.9990 chunk 284 optimal weight: 0.0980 chunk 234 optimal weight: 0.8980 chunk 260 optimal weight: 0.7980 chunk 89 optimal weight: 0.4980 chunk 210 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN E 216 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 ASN I 327 HIS J 112 GLN K 47 ASN ** 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: 0.1929 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24443 Z= 0.171 Angle : 0.625 11.600 33270 Z= 0.323 Chirality : 0.045 0.268 3694 Planarity : 0.004 0.054 4206 Dihedral : 14.766 173.530 3891 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 2.09 % Allowed : 14.46 % Favored : 83.45 % 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: 0.32 (0.16), residues: 2862 helix: 1.38 (0.17), residues: 956 sheet: 0.29 (0.21), residues: 570 loop : -0.64 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 40 HIS 0.005 0.001 HIS F 179 PHE 0.020 0.002 PHE B 113 TYR 0.018 0.001 TYR B 68 ARG 0.006 0.000 ARG B 268 *********************** 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 284 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 233 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.6892 (ttt) cc_final: 0.6624 (ttt) REVERT: B 140 PHE cc_start: 0.6642 (m-10) cc_final: 0.6240 (m-10) REVERT: C 30 MET cc_start: 0.0900 (mtp) cc_final: -0.0544 (mtp) REVERT: C 123 MET cc_start: -0.1740 (ptp) cc_final: -0.2452 (mtm) REVERT: C 138 MET cc_start: 0.3588 (ppp) cc_final: 0.1828 (ppp) REVERT: C 289 MET cc_start: 0.5588 (ppp) cc_final: 0.4839 (pmm) REVERT: E 138 MET cc_start: 0.3066 (mtt) cc_final: 0.1588 (mpp) REVERT: F 229 MET cc_start: 0.2210 (mtp) cc_final: 0.1898 (mtp) REVERT: G 138 MET cc_start: -0.2169 (ptp) cc_final: -0.3197 (mtm) REVERT: G 272 ASP cc_start: 0.5247 (m-30) cc_final: 0.4881 (t0) REVERT: H 157 MET cc_start: 0.3464 (tmm) cc_final: 0.2820 (pmm) REVERT: I 343 MET cc_start: -0.3017 (mtp) cc_final: -0.4312 (tpt) REVERT: I 346 MET cc_start: -0.1239 (OUTLIER) cc_final: -0.2248 (mmm) REVERT: I 514 GLU cc_start: 0.1316 (pt0) cc_final: 0.0767 (tt0) REVERT: J 82 MET cc_start: 0.1225 (mtm) cc_final: 0.0025 (tmm) REVERT: K 97 MET cc_start: -0.1184 (mmp) cc_final: -0.1969 (mpp) outliers start: 51 outliers final: 29 residues processed: 269 average time/residue: 0.3533 time to fit residues: 149.8921 Evaluate side-chains 237 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 207 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 268 THR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 353 HIS Chi-restraints excluded: chain I residue 517 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 77 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 259 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 125 optimal weight: 0.2980 chunk 176 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN C 241 ASN D 70 GLN D 150 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** E 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 ASN F 29 ASN G 179 HIS ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 221 ASN I 258 ASN I 546 ASN J 62 HIS J 112 GLN K 47 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2904 moved from start: 0.8033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 24443 Z= 0.331 Angle : 0.882 15.187 33270 Z= 0.462 Chirality : 0.053 0.277 3694 Planarity : 0.007 0.075 4206 Dihedral : 15.253 169.802 3891 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.30 % Rotamer: Outliers : 3.65 % Allowed : 16.67 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.26 (0.16), residues: 955 sheet: 0.00 (0.23), residues: 496 loop : -1.12 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP M 40 HIS 0.015 0.002 HIS I 327 PHE 0.036 0.003 PHE B 113 TYR 0.027 0.003 TYR C 186 ARG 0.013 0.001 ARG I 448 *********************** 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 348 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 259 time to evaluate : 2.676 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: A 201 MET cc_start: 0.8234 (mtm) cc_final: 0.7917 (mtt) REVERT: B 1 MET cc_start: 0.2366 (OUTLIER) cc_final: 0.1622 (ppp) REVERT: B 217 MET cc_start: 0.6421 (mmt) cc_final: 0.6178 (mmt) REVERT: C 138 MET cc_start: 0.4731 (OUTLIER) cc_final: 0.3275 (ptt) REVERT: D 109 MET cc_start: -0.0402 (mmt) cc_final: -0.1883 (mtt) REVERT: D 240 GLN cc_start: -0.0731 (OUTLIER) cc_final: -0.1035 (mm-40) REVERT: E 109 MET cc_start: -0.0881 (mmm) cc_final: -0.1622 (mtm) REVERT: F 217 MET cc_start: 0.1327 (mtm) cc_final: 0.0628 (mtp) REVERT: G 123 MET cc_start: 0.1394 (ptp) cc_final: 0.0718 (ppp) REVERT: H 157 MET cc_start: 0.3438 (tmm) cc_final: 0.2323 (mmp) REVERT: I 192 LYS cc_start: 0.6813 (OUTLIER) cc_final: 0.6169 (mmtm) REVERT: I 286 MET cc_start: 0.2205 (ptp) cc_final: 0.1950 (ptm) REVERT: I 343 MET cc_start: -0.2762 (mtp) cc_final: -0.4162 (tpt) REVERT: I 346 MET cc_start: -0.1289 (OUTLIER) cc_final: -0.2154 (mmm) REVERT: I 570 MET cc_start: 0.2498 (mtt) cc_final: 0.2221 (mtt) REVERT: I 571 MET cc_start: 0.1905 (mmp) cc_final: 0.1339 (tpp) REVERT: I 594 MET cc_start: 0.1510 (OUTLIER) cc_final: 0.0824 (tmm) outliers start: 89 outliers final: 50 residues processed: 325 average time/residue: 0.3474 time to fit residues: 177.6496 Evaluate side-chains 281 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 225 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 240 GLN Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 189 HIS Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 268 THR Chi-restraints excluded: chain I residue 281 ASP Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 578 ILE Chi-restraints excluded: chain I residue 594 MET Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain M residue 13 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 232 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 142 optimal weight: 0.0050 chunk 250 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 112 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN D 239 HIS ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 GLN I 535 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3209 moved from start: 0.9471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24443 Z= 0.296 Angle : 0.780 14.246 33270 Z= 0.405 Chirality : 0.049 0.235 3694 Planarity : 0.006 0.069 4206 Dihedral : 15.018 177.776 3891 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 3.89 % Allowed : 17.74 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.81 (0.15), residues: 2862 helix: 0.39 (0.16), residues: 954 sheet: -0.42 (0.22), residues: 517 loop : -1.21 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP M 40 HIS 0.008 0.002 HIS I 541 PHE 0.038 0.003 PHE J 105 TYR 0.034 0.003 TYR B 68 ARG 0.021 0.001 ARG G 156 *********************** 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 353 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 258 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8431 (mtm) cc_final: 0.8098 (mtt) REVERT: B 1 MET cc_start: 0.2830 (OUTLIER) cc_final: 0.2378 (ppp) REVERT: B 68 TYR cc_start: 0.5369 (OUTLIER) cc_final: 0.4331 (m-80) REVERT: B 186 TYR cc_start: 0.8841 (m-80) cc_final: 0.8514 (m-80) REVERT: B 220 HIS cc_start: 0.1553 (OUTLIER) cc_final: 0.1296 (m170) REVERT: C 7 ARG cc_start: 0.6303 (ttp-170) cc_final: 0.5841 (ttp-170) REVERT: C 138 MET cc_start: 0.4717 (OUTLIER) cc_final: 0.2803 (mmm) REVERT: C 273 TYR cc_start: 0.4727 (m-80) cc_final: 0.3841 (m-80) REVERT: E 109 MET cc_start: -0.0821 (mmm) cc_final: -0.1425 (mtm) REVERT: E 242 ARG cc_start: 0.3898 (ptm160) cc_final: 0.2761 (tpt-90) REVERT: E 288 GLU cc_start: 0.2375 (OUTLIER) cc_final: 0.2003 (mp0) REVERT: F 179 HIS cc_start: 0.4416 (m-70) cc_final: 0.4147 (m-70) REVERT: F 241 ASN cc_start: 0.1261 (OUTLIER) cc_final: 0.0900 (m-40) REVERT: H 76 ASN cc_start: 0.3177 (m-40) cc_final: 0.1806 (p0) REVERT: H 157 MET cc_start: 0.3527 (tmm) cc_final: 0.2452 (mmt) REVERT: H 205 GLU cc_start: 0.5247 (mp0) cc_final: 0.4651 (pt0) REVERT: I 187 THR cc_start: 0.6718 (OUTLIER) cc_final: 0.6405 (p) REVERT: I 192 LYS cc_start: 0.7186 (pttt) cc_final: 0.6670 (mmtm) REVERT: I 343 MET cc_start: -0.2338 (mtp) cc_final: -0.3385 (tpt) REVERT: I 346 MET cc_start: -0.1366 (OUTLIER) cc_final: -0.2206 (tpp) REVERT: K 5 PRO cc_start: 0.8231 (Cg_endo) cc_final: 0.7882 (Cg_exo) REVERT: M 1 MET cc_start: 0.0551 (mtm) cc_final: 0.0346 (mtm) outliers start: 95 outliers final: 52 residues processed: 335 average time/residue: 0.3318 time to fit residues: 178.4499 Evaluate side-chains 292 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 232 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 268 THR Chi-restraints excluded: chain I residue 281 ASP Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 448 ARG Chi-restraints excluded: chain I residue 492 ASP Chi-restraints excluded: chain I residue 517 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 592 LEU Chi-restraints excluded: chain I residue 597 TYR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 93 optimal weight: 0.2980 chunk 251 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 164 optimal weight: 0.0770 chunk 68 optimal weight: 0.3980 chunk 279 optimal weight: 0.8980 chunk 232 optimal weight: 20.0000 chunk 129 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 HIS ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3059 moved from start: 0.9580 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= 0.169 Angle : 0.627 12.540 33270 Z= 0.324 Chirality : 0.045 0.209 3694 Planarity : 0.005 0.060 4206 Dihedral : 14.463 179.368 3891 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 2.29 % Allowed : 19.38 % Favored : 78.33 % 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: -0.34 (0.15), residues: 2862 helix: 0.88 (0.17), residues: 962 sheet: -0.22 (0.22), residues: 506 loop : -0.99 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 211 HIS 0.007 0.001 HIS D 54 PHE 0.025 0.002 PHE H 210 TYR 0.020 0.002 TYR H 273 ARG 0.007 0.000 ARG H 142 *********************** 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 299 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 243 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8268 (mtm) cc_final: 0.8037 (mtt) REVERT: B 1 MET cc_start: 0.2946 (OUTLIER) cc_final: 0.2580 (ppp) REVERT: B 68 TYR cc_start: 0.5375 (OUTLIER) cc_final: 0.4092 (m-80) REVERT: C 7 ARG cc_start: 0.5811 (ttp-170) cc_final: 0.5330 (ttp-170) REVERT: C 138 MET cc_start: 0.4159 (OUTLIER) cc_final: 0.3005 (ppp) REVERT: D 69 ILE cc_start: 0.2049 (OUTLIER) cc_final: 0.1737 (mt) REVERT: D 109 MET cc_start: 0.0139 (mmt) cc_final: -0.0961 (mtp) REVERT: E 109 MET cc_start: -0.0621 (mmm) cc_final: -0.1135 (mtm) REVERT: E 242 ARG cc_start: 0.3735 (ptm160) cc_final: 0.1867 (ptt-90) REVERT: F 179 HIS cc_start: 0.4080 (m-70) cc_final: 0.3858 (m-70) REVERT: H 2 THR cc_start: -0.1347 (OUTLIER) cc_final: -0.1679 (m) REVERT: H 157 MET cc_start: 0.3694 (tmm) cc_final: 0.2599 (mmt) REVERT: H 205 GLU cc_start: 0.5283 (mp0) cc_final: 0.4730 (pt0) REVERT: I 192 LYS cc_start: 0.6997 (pttt) cc_final: 0.6599 (mmtm) REVERT: I 343 MET cc_start: -0.2993 (mtp) cc_final: -0.3969 (tpt) REVERT: I 346 MET cc_start: -0.1005 (OUTLIER) cc_final: -0.2513 (tpp) REVERT: I 571 MET cc_start: 0.1777 (mmp) cc_final: 0.1329 (tpp) REVERT: I 594 MET cc_start: 0.0985 (tpp) cc_final: 0.0588 (tmm) REVERT: J 111 HIS cc_start: 0.2043 (OUTLIER) cc_final: -0.0733 (p90) REVERT: K 5 PRO cc_start: 0.8401 (Cg_endo) cc_final: 0.8026 (Cg_exo) REVERT: M 51 GLU cc_start: 0.4889 (OUTLIER) cc_final: 0.4599 (mp0) outliers start: 56 outliers final: 32 residues processed: 288 average time/residue: 0.3381 time to fit residues: 158.8401 Evaluate side-chains 262 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 222 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 364 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain M residue 31 TRP Chi-restraints excluded: chain M residue 36 MET Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 269 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 235 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 169 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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** ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 HIS ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 538 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3581 moved from start: 1.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 24443 Z= 0.308 Angle : 0.831 15.218 33270 Z= 0.435 Chirality : 0.051 0.435 3694 Planarity : 0.007 0.078 4206 Dihedral : 14.694 173.320 3891 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.39 % Favored : 93.57 % Rotamer: Outliers : 3.65 % Allowed : 19.46 % Favored : 76.89 % 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: -1.06 (0.15), residues: 2862 helix: 0.17 (0.16), residues: 946 sheet: -0.51 (0.23), residues: 500 loop : -1.36 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP M 40 HIS 0.016 0.002 HIS E 39 PHE 0.035 0.003 PHE K 105 TYR 0.030 0.003 TYR B 183 ARG 0.013 0.001 ARG J 113 *********************** 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 330 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 241 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.8379 (m-80) cc_final: 0.8153 (m-80) REVERT: B 68 TYR cc_start: 0.5930 (OUTLIER) cc_final: 0.5011 (m-80) REVERT: B 157 MET cc_start: 0.1922 (mtp) cc_final: 0.1541 (mtp) REVERT: B 187 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8781 (t) REVERT: B 220 HIS cc_start: 0.2296 (OUTLIER) cc_final: 0.2069 (m170) REVERT: C 7 ARG cc_start: 0.6231 (ttp-170) cc_final: 0.5546 (ttp-170) REVERT: C 138 MET cc_start: 0.4706 (OUTLIER) cc_final: 0.3495 (mmm) REVERT: C 289 MET cc_start: 0.3315 (pmm) cc_final: 0.1906 (tmm) REVERT: E 109 MET cc_start: -0.0211 (mmm) cc_final: -0.1563 (mtt) REVERT: F 9 GLU cc_start: 0.0741 (OUTLIER) cc_final: -0.1024 (mt-10) REVERT: F 191 PHE cc_start: 0.4080 (OUTLIER) cc_final: 0.3671 (m-80) REVERT: F 229 MET cc_start: 0.1390 (ttm) cc_final: 0.0934 (ttm) REVERT: G 138 MET cc_start: 0.0893 (mpp) cc_final: 0.0539 (mpp) REVERT: H 2 THR cc_start: -0.0987 (OUTLIER) cc_final: -0.1232 (m) REVERT: H 157 MET cc_start: 0.3751 (tmm) cc_final: 0.2618 (mmp) REVERT: H 205 GLU cc_start: 0.5211 (mp0) cc_final: 0.4840 (pt0) REVERT: H 217 MET cc_start: 0.6343 (ppp) cc_final: 0.5498 (ppp) REVERT: H 290 LEU cc_start: 0.0564 (OUTLIER) cc_final: 0.0248 (mt) REVERT: I 246 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.6570 (p90) REVERT: I 343 MET cc_start: -0.2883 (mtp) cc_final: -0.4151 (tpt) REVERT: I 346 MET cc_start: -0.1425 (OUTLIER) cc_final: -0.1651 (mmp) REVERT: I 571 MET cc_start: 0.1858 (mmp) cc_final: 0.1326 (tpp) REVERT: K 5 PRO cc_start: 0.8715 (Cg_endo) cc_final: 0.8492 (Cg_exo) REVERT: M 31 TRP cc_start: 0.0256 (OUTLIER) cc_final: -0.0495 (t60) REVERT: M 51 GLU cc_start: 0.5104 (OUTLIER) cc_final: 0.4607 (mp0) outliers start: 89 outliers final: 52 residues processed: 315 average time/residue: 0.3425 time to fit residues: 174.7606 Evaluate side-chains 280 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 216 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 281 ASP Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 417 GLU Chi-restraints excluded: chain I residue 492 ASP Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 597 TYR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 31 TRP Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 177 optimal weight: 8.9990 chunk 189 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 218 optimal weight: 0.6980 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 108 GLN B 112 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 ASN ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 538 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3454 moved from start: 1.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 24443 Z= 0.200 Angle : 0.660 14.390 33270 Z= 0.340 Chirality : 0.046 0.321 3694 Planarity : 0.005 0.059 4206 Dihedral : 14.385 176.735 3891 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 2.66 % Allowed : 20.40 % Favored : 76.94 % 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: 0.57 (0.16), residues: 950 sheet: -0.39 (0.23), residues: 483 loop : -1.19 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 211 HIS 0.015 0.001 HIS J 53 PHE 0.026 0.002 PHE H 210 TYR 0.030 0.002 TYR G 8 ARG 0.006 0.000 ARG A 116 *********************** 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 307 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 242 time to evaluate : 2.504 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: A 142 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7764 (tt) REVERT: B 68 TYR cc_start: 0.5915 (OUTLIER) cc_final: 0.4824 (m-80) REVERT: B 157 MET cc_start: 0.2048 (mtp) cc_final: 0.1720 (mtp) REVERT: C 7 ARG cc_start: 0.5711 (ttp-170) cc_final: 0.5035 (ttp-170) REVERT: C 289 MET cc_start: 0.3029 (pmm) cc_final: 0.1830 (tmm) REVERT: E 109 MET cc_start: -0.0646 (mmm) cc_final: -0.1927 (mtt) REVERT: E 242 ARG cc_start: 0.3714 (ptm160) cc_final: 0.1814 (ptt-90) REVERT: F 117 ARG cc_start: 0.0427 (OUTLIER) cc_final: -0.0214 (ttm-80) REVERT: F 191 PHE cc_start: 0.4134 (OUTLIER) cc_final: 0.3624 (m-80) REVERT: F 229 MET cc_start: 0.1216 (ttm) cc_final: 0.0781 (ttm) REVERT: G 138 MET cc_start: 0.1131 (mpp) cc_final: -0.0697 (ttm) REVERT: H 2 THR cc_start: -0.1136 (OUTLIER) cc_final: -0.1365 (m) REVERT: H 157 MET cc_start: 0.3834 (tmm) cc_final: 0.2566 (mmp) REVERT: H 205 GLU cc_start: 0.5270 (mp0) cc_final: 0.4941 (pt0) REVERT: H 217 MET cc_start: 0.6392 (ppp) cc_final: 0.5796 (ppp) REVERT: H 290 LEU cc_start: 0.0728 (OUTLIER) cc_final: -0.0028 (mt) REVERT: I 343 MET cc_start: -0.2977 (mtp) cc_final: -0.3974 (tpt) REVERT: I 346 MET cc_start: -0.1419 (OUTLIER) cc_final: -0.2338 (mmm) REVERT: I 542 MET cc_start: 0.2299 (ppp) cc_final: 0.0965 (ppp) REVERT: I 571 MET cc_start: 0.1731 (mmp) cc_final: 0.1312 (tpp) REVERT: K 5 PRO cc_start: 0.8761 (Cg_endo) cc_final: 0.8559 (Cg_exo) REVERT: M 31 TRP cc_start: 0.0184 (OUTLIER) cc_final: -0.0485 (t60) outliers start: 65 outliers final: 42 residues processed: 297 average time/residue: 0.3402 time to fit residues: 163.0176 Evaluate side-chains 266 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 216 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 281 ASP Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain I residue 597 TYR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 31 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 253 optimal weight: 0.0040 chunk 266 optimal weight: 0.6980 chunk 243 optimal weight: 0.0770 chunk 259 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 79 optimal weight: 0.4980 chunk 234 optimal weight: 0.6980 chunk 245 optimal weight: 7.9990 chunk 258 optimal weight: 0.0170 overall best weight: 0.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 112 ASN B 131 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS C 76 ASN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN G 18 ASN ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 ASN ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3300 moved from start: 1.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24443 Z= 0.161 Angle : 0.628 13.310 33270 Z= 0.322 Chirality : 0.044 0.302 3694 Planarity : 0.005 0.052 4206 Dihedral : 14.180 178.863 3891 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.70 % Rotamer: Outliers : 2.13 % Allowed : 20.93 % Favored : 76.94 % 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: -0.34 (0.15), residues: 2862 helix: 0.90 (0.17), residues: 956 sheet: -0.03 (0.23), residues: 483 loop : -1.07 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 211 HIS 0.015 0.001 HIS H 54 PHE 0.025 0.002 PHE H 210 TYR 0.022 0.001 TYR G 8 ARG 0.004 0.000 ARG C 259 *********************** 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 296 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 244 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7751 (tt) REVERT: B 30 MET cc_start: 0.6900 (mmm) cc_final: 0.6594 (mmm) REVERT: B 68 TYR cc_start: 0.5696 (OUTLIER) cc_final: 0.4569 (m-80) REVERT: B 123 MET cc_start: 0.4126 (mmt) cc_final: 0.2569 (mmt) REVERT: C 7 ARG cc_start: 0.5570 (ttp-170) cc_final: 0.4980 (ttp-170) REVERT: C 17 GLU cc_start: 0.2186 (tm-30) cc_final: 0.1673 (mp0) REVERT: C 123 MET cc_start: 0.0283 (mpp) cc_final: 0.0040 (mpp) REVERT: C 138 MET cc_start: 0.4062 (ppp) cc_final: 0.3060 (mtt) REVERT: C 289 MET cc_start: 0.3310 (pmm) cc_final: 0.2317 (tmm) REVERT: D 69 ILE cc_start: 0.2064 (OUTLIER) cc_final: 0.1723 (mt) REVERT: D 289 MET cc_start: 0.3960 (ptm) cc_final: 0.3647 (ptm) REVERT: E 109 MET cc_start: -0.0609 (mmm) cc_final: -0.1844 (mtt) REVERT: E 242 ARG cc_start: 0.3377 (ptm160) cc_final: 0.1612 (ptt-90) REVERT: G 123 MET cc_start: 0.0866 (ptp) cc_final: 0.0194 (ppp) REVERT: G 138 MET cc_start: 0.0777 (mpp) cc_final: -0.0691 (ttm) REVERT: H 157 MET cc_start: 0.3664 (tmm) cc_final: 0.2470 (mmp) REVERT: H 205 GLU cc_start: 0.5224 (mp0) cc_final: 0.4978 (pt0) REVERT: H 210 PHE cc_start: 0.3520 (t80) cc_final: 0.3214 (t80) REVERT: H 217 MET cc_start: 0.6423 (ppp) cc_final: 0.6096 (ppp) REVERT: H 290 LEU cc_start: 0.0256 (OUTLIER) cc_final: -0.0005 (mt) REVERT: I 326 MET cc_start: 0.2416 (tpt) cc_final: -0.1172 (ptt) REVERT: I 343 MET cc_start: -0.2994 (mtp) cc_final: -0.3910 (tpt) REVERT: I 346 MET cc_start: -0.1384 (OUTLIER) cc_final: -0.2315 (mmm) REVERT: I 542 MET cc_start: 0.1966 (ppp) cc_final: 0.1318 (ppp) REVERT: I 571 MET cc_start: 0.1896 (mmp) cc_final: 0.1312 (tpp) REVERT: J 111 HIS cc_start: 0.1718 (OUTLIER) cc_final: -0.0770 (p90) REVERT: M 31 TRP cc_start: -0.0164 (OUTLIER) cc_final: -0.0615 (t60) outliers start: 52 outliers final: 32 residues processed: 287 average time/residue: 0.3504 time to fit residues: 161.5265 Evaluate side-chains 256 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 217 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 281 ASP Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 597 TYR Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain M residue 31 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 287 optimal weight: 0.0010 chunk 264 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 112 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 ASN ** I 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 GLN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3429 moved from start: 1.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24443 Z= 0.182 Angle : 0.649 13.965 33270 Z= 0.331 Chirality : 0.045 0.267 3694 Planarity : 0.005 0.058 4206 Dihedral : 14.148 177.556 3891 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 1.84 % Allowed : 21.34 % Favored : 76.81 % 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: -0.32 (0.15), residues: 2862 helix: 0.92 (0.17), residues: 956 sheet: -0.04 (0.22), residues: 512 loop : -1.07 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 369 HIS 0.012 0.001 HIS J 53 PHE 0.024 0.002 PHE I 540 TYR 0.024 0.002 TYR G 8 ARG 0.014 0.000 ARG G 226 ********************** 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 273 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7161 (pttt) cc_final: 0.6933 (tmmt) REVERT: A 142 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7756 (tt) REVERT: B 68 TYR cc_start: 0.5923 (OUTLIER) cc_final: 0.4776 (m-80) REVERT: B 123 MET cc_start: 0.4545 (mmt) cc_final: 0.2816 (mmt) REVERT: C 123 MET cc_start: 0.0358 (mpp) cc_final: 0.0104 (mpp) REVERT: C 289 MET cc_start: 0.3234 (pmm) cc_final: 0.2615 (tmm) REVERT: E 109 MET cc_start: -0.0542 (mmm) cc_final: -0.1909 (mtt) REVERT: E 242 ARG cc_start: 0.3465 (ptm160) cc_final: 0.1632 (ptt-90) REVERT: F 117 ARG cc_start: 0.0651 (OUTLIER) cc_final: 0.0017 (ttm-80) REVERT: G 138 MET cc_start: 0.0824 (mpp) cc_final: -0.0670 (ttm) REVERT: H 52 ARG cc_start: 0.3488 (ptt180) cc_final: 0.3057 (mtm180) REVERT: H 157 MET cc_start: 0.3642 (tmm) cc_final: 0.2461 (mmp) REVERT: H 290 LEU cc_start: 0.0491 (OUTLIER) cc_final: 0.0230 (mt) REVERT: I 244 PHE cc_start: 0.5774 (t80) cc_final: 0.5440 (t80) REVERT: I 326 MET cc_start: 0.2547 (tpt) cc_final: -0.1080 (ptt) REVERT: I 343 MET cc_start: -0.2866 (mtp) cc_final: -0.3843 (tpt) REVERT: I 346 MET cc_start: -0.1502 (OUTLIER) cc_final: -0.2402 (mmm) REVERT: I 542 MET cc_start: 0.2364 (ppp) cc_final: 0.1916 (ptp) REVERT: I 571 MET cc_start: 0.1879 (mmp) cc_final: 0.1274 (tpp) REVERT: J 111 HIS cc_start: 0.1771 (OUTLIER) cc_final: -0.0773 (p90) REVERT: K 106 MET cc_start: 0.2268 (mpp) cc_final: 0.0881 (ptp) REVERT: M 31 TRP cc_start: 0.0621 (OUTLIER) cc_final: 0.0092 (t60) outliers start: 45 outliers final: 32 residues processed: 267 average time/residue: 0.3501 time to fit residues: 148.4238 Evaluate side-chains 249 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 210 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 281 ASP Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 597 TYR Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain M residue 31 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 182 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 211 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 235 optimal weight: 0.0970 chunk 29 optimal weight: 7.9990 chunk 42 optimal weight: 0.0370 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 112 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5190 r_free = 0.5190 target = 0.294033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.275129 restraints weight = 41186.378| |-----------------------------------------------------------------------------| r_work (start): 0.5034 rms_B_bonded: 2.38 r_work: 0.4969 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3784 moved from start: 1.1830 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= 0.172 Angle : 0.633 12.889 33270 Z= 0.322 Chirality : 0.044 0.266 3694 Planarity : 0.005 0.085 4206 Dihedral : 14.105 178.254 3891 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.60 % Rotamer: Outliers : 1.88 % Allowed : 21.43 % Favored : 76.69 % 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: -0.23 (0.15), residues: 2862 helix: 0.99 (0.17), residues: 955 sheet: 0.05 (0.23), residues: 487 loop : -1.01 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 369 HIS 0.011 0.001 HIS J 53 PHE 0.025 0.002 PHE H 218 TYR 0.022 0.001 TYR G 8 ARG 0.011 0.000 ARG G 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5194.37 seconds wall clock time: 94 minutes 31.80 seconds (5671.80 seconds total)