Starting phenix.real_space_refine on Mon Dec 11 18:00:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/12_2023/3j7a_2660_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/12_2023/3j7a_2660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/12_2023/3j7a_2660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/12_2023/3j7a_2660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/12_2023/3j7a_2660_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/12_2023/3j7a_2660_updated.pdb" } resolution = 3.2 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= 0.044 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1681 5.49 5 Mg 67 5.21 5 S 141 5.16 5 C 37011 2.51 5 N 12467 2.21 5 O 17498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "E ARG 13": "NH1" <-> "NH2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 78": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "E ARG 130": "NH1" <-> "NH2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 178": "NH1" <-> "NH2" Residue "G ARG 180": "NH1" <-> "NH2" Residue "G GLU 253": "OE1" <-> "OE2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H ARG 154": "NH1" <-> "NH2" Residue "H GLU 200": "OE1" <-> "OE2" Residue "I ARG 46": "NH1" <-> "NH2" Residue "I ARG 53": "NH1" <-> "NH2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "I ARG 150": "NH1" <-> "NH2" Residue "I ARG 155": "NH1" <-> "NH2" Residue "I GLU 186": "OE1" <-> "OE2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "J GLU 17": "OE1" <-> "OE2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J GLU 128": "OE1" <-> "OE2" Residue "J ARG 140": "NH1" <-> "NH2" Residue "J GLU 159": "OE1" <-> "OE2" Residue "J ARG 160": "NH1" <-> "NH2" Residue "J ARG 182": "NH1" <-> "NH2" Residue "K ARG 3": "NH1" <-> "NH2" Residue "K GLU 51": "OE1" <-> "OE2" Residue "K ARG 68": "NH1" <-> "NH2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K GLU 114": "OE1" <-> "OE2" Residue "K GLU 115": "OE1" <-> "OE2" Residue "L ARG 12": "NH1" <-> "NH2" Residue "L ARG 51": "NH1" <-> "NH2" Residue "L ARG 210": "NH1" <-> "NH2" Residue "L ARG 217": "NH1" <-> "NH2" Residue "M ARG 124": "NH1" <-> "NH2" Residue "M ARG 138": "NH1" <-> "NH2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "N GLU 71": "OE1" <-> "OE2" Residue "N ARG 78": "NH1" <-> "NH2" Residue "N ARG 82": "NH1" <-> "NH2" Residue "N ARG 86": "NH1" <-> "NH2" Residue "N GLU 112": "OE1" <-> "OE2" Residue "O GLU 67": "OE1" <-> "OE2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "P ARG 55": "NH1" <-> "NH2" Residue "P ARG 66": "NH1" <-> "NH2" Residue "P ARG 117": "NH1" <-> "NH2" Residue "P ARG 121": "NH1" <-> "NH2" Residue "P ARG 128": "NH1" <-> "NH2" Residue "P ARG 141": "NH1" <-> "NH2" Residue "P ARG 146": "NH1" <-> "NH2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P ARG 149": "NH1" <-> "NH2" Residue "P ARG 150": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 16": "NH1" <-> "NH2" Residue "Q ARG 19": "NH1" <-> "NH2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "Q ARG 73": "NH1" <-> "NH2" Residue "Q GLU 98": "OE1" <-> "OE2" Residue "Q GLU 138": "OE1" <-> "OE2" Residue "Q GLU 141": "OE1" <-> "OE2" Residue "S GLU 26": "OE1" <-> "OE2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 89": "NH1" <-> "NH2" Residue "S ARG 115": "NH1" <-> "NH2" Residue "S ARG 123": "NH1" <-> "NH2" Residue "T ARG 38": "NH1" <-> "NH2" Residue "T ARG 54": "NH1" <-> "NH2" Residue "U GLU 32": "OE1" <-> "OE2" Residue "U GLU 34": "OE1" <-> "OE2" Residue "U ARG 55": "NH1" <-> "NH2" Residue "U ARG 73": "NH1" <-> "NH2" Residue "U ARG 124": "NH1" <-> "NH2" Residue "U ARG 131": "NH1" <-> "NH2" Residue "V ARG 11": "NH1" <-> "NH2" Residue "V ARG 36": "NH1" <-> "NH2" Residue "V ARG 91": "NH1" <-> "NH2" Residue "V GLU 146": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W ARG 67": "NH1" <-> "NH2" Residue "W GLU 77": "OE1" <-> "OE2" Residue "X ARG 43": "NH1" <-> "NH2" Residue "X ARG 47": "NH1" <-> "NH2" Residue "X GLU 88": "OE1" <-> "OE2" Residue "Y ARG 15": "NH1" <-> "NH2" Residue "Y ARG 66": "NH1" <-> "NH2" Residue "Y GLU 73": "OE1" <-> "OE2" Residue "Y ARG 79": "NH1" <-> "NH2" Residue "Y ARG 99": "NH1" <-> "NH2" Residue "Y ARG 124": "NH1" <-> "NH2" Residue "Y GLU 131": "OE1" <-> "OE2" Residue "Y ARG 146": "NH1" <-> "NH2" Residue "Y GLU 152": "OE1" <-> "OE2" Residue "Y ARG 160": "NH1" <-> "NH2" Residue "Z GLU 28": "OE1" <-> "OE2" Residue "Z ARG 70": "NH1" <-> "NH2" Residue "1 ARG 20": "NH1" <-> "NH2" Residue "1 GLU 87": "OE1" <-> "OE2" Residue "1 ARG 91": "NH1" <-> "NH2" Residue "1 ARG 106": "NH1" <-> "NH2" Residue "3 ARG 6": "NH1" <-> "NH2" Residue "3 ARG 42": "NH1" <-> "NH2" Residue "3 ARG 51": "NH1" <-> "NH2" Residue "3 GLU 90": "OE1" <-> "OE2" Residue "3 ARG 92": "NH1" <-> "NH2" Residue "3 ARG 93": "NH1" <-> "NH2" Residue "4 GLU 13": "OE1" <-> "OE2" Residue "4 GLU 82": "OE1" <-> "OE2" Residue "5 ARG 15": "NH1" <-> "NH2" Residue "5 ARG 38": "NH1" <-> "NH2" Residue "6 ARG 33": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 68866 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 34277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1608, 34277 Classifications: {'RNA': 1608} Modifications used: {'rna2p_pur': 137, 'rna2p_pyr': 92, 'rna3p_pur': 738, 'rna3p_pyr': 641} Link IDs: {'rna2p': 228, 'rna3p': 1379} Chain breaks: 22 Chain: "B" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1713 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain: "C" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "D" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1228 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 3 Chain: "E" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1508 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2061 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain: "G" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1757 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "H" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1644 Classifications: {'peptide': 204} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1424 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "J" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1528 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain: "K" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1037 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1392 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 2 Chain: "M" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1098 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "N" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 772 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "O" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 686 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "P" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 953 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "Q" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1129 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "R" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 746 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain breaks: 2 Chain: "S" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1042 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 404 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "U" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 141} Chain: "V" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1206 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain breaks: 1 Chain: "W" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain breaks: 1 Chain: "X" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 776 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain breaks: 1 Chain: "Y" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1266 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain: "Z" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 556 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "1" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 981 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "2" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 320 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 2 Chain: "3" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 781 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "4" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 586 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "5" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 451 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "6" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 345 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "7" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1571 Classifications: {'RNA': 74} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 31, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 62} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 102 Unusual residues: {' MG': 67, '34G': 1} Classifications: {'undetermined': 68} Link IDs: {None: 67} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 57636 SG CYS T 19 55.402 88.444 75.019 1.00119.06 S ATOM 57660 SG CYS T 22 58.256 92.212 74.720 1.00187.39 S ATOM 57784 SG CYS T 37 58.819 87.359 76.500 1.00132.78 S ATOM 57810 SG CYS T 40 58.234 90.449 77.786 1.00141.95 S Time building chain proxies: 26.47, per 1000 atoms: 0.38 Number of scatterers: 68866 At special positions: 0 Unit cell: (218.42, 226.46, 192.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 141 16.00 P 1681 15.00 Mg 67 11.99 O 17498 8.00 N 12467 7.00 C 37011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 3 26 " - pdb=" SG CYS 3 77 " distance=2.04 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: 28.21 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN T 100 " pdb="ZN ZN T 100 " - pdb=" SG CYS T 40 " pdb="ZN ZN T 100 " - pdb=" SG CYS T 37 " pdb="ZN ZN T 100 " - pdb=" SG CYS T 22 " pdb="ZN ZN T 100 " - pdb=" SG CYS T 19 " Number of angles added : 6 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 142 helices and 45 sheets defined 33.3% alpha, 11.5% beta 482 base pairs and 897 stacking pairs defined. Time for finding SS restraints: 27.10 Creating SS restraints... Processing helix chain 'B' and resid 58 through 61 No H-bonds generated for 'chain 'B' and resid 58 through 61' Processing helix chain 'B' and resid 71 through 74 No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 158 through 178 Processing helix chain 'B' and resid 181 through 189 Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'C' and resid 11 through 19 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 51 through 66 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 80 through 92 removed outlier: 4.579A pdb=" N ARG C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA C 85 " --> pdb=" O PHE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 139 removed outlier: 3.616A pdb=" N ALA C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 184 Processing helix chain 'D' and resid 7 through 28 Processing helix chain 'D' and resid 67 through 77 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'E' and resid 21 through 34 Processing helix chain 'E' and resid 40 through 61 removed outlier: 3.538A pdb=" N ILE E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 83 Processing helix chain 'E' and resid 101 through 107 removed outlier: 3.877A pdb=" N ARG E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 115 Processing helix chain 'E' and resid 122 through 130 Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 173 through 185 Processing helix chain 'F' and resid 16 through 18 No H-bonds generated for 'chain 'F' and resid 16 through 18' Processing helix chain 'F' and resid 38 through 40 No H-bonds generated for 'chain 'F' and resid 38 through 40' Processing helix chain 'F' and resid 44 through 49 Processing helix chain 'F' and resid 58 through 66 Processing helix chain 'F' and resid 116 through 120 removed outlier: 3.582A pdb=" N LYS F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 116 through 120' Processing helix chain 'F' and resid 222 through 224 No H-bonds generated for 'chain 'F' and resid 222 through 224' Processing helix chain 'F' and resid 248 through 256 Processing helix chain 'G' and resid 46 through 52 Processing helix chain 'G' and resid 59 through 64 Processing helix chain 'G' and resid 72 through 78 Processing helix chain 'G' and resid 133 through 147 Processing helix chain 'G' and resid 194 through 203 Processing helix chain 'G' and resid 219 through 233 Processing helix chain 'G' and resid 239 through 242 removed outlier: 3.817A pdb=" N TRP G 242 " --> pdb=" O PRO G 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 239 through 242' Processing helix chain 'G' and resid 251 through 254 No H-bonds generated for 'chain 'G' and resid 251 through 254' Processing helix chain 'G' and resid 256 through 259 No H-bonds generated for 'chain 'G' and resid 256 through 259' Processing helix chain 'H' and resid 21 through 24 No H-bonds generated for 'chain 'H' and resid 21 through 24' Processing helix chain 'H' and resid 38 through 40 No H-bonds generated for 'chain 'H' and resid 38 through 40' Processing helix chain 'H' and resid 138 through 145 Processing helix chain 'H' and resid 181 through 212 Processing helix chain 'I' and resid 25 through 29 Processing helix chain 'I' and resid 53 through 56 No H-bonds generated for 'chain 'I' and resid 53 through 56' Processing helix chain 'I' and resid 59 through 67 Processing helix chain 'I' and resid 71 through 73 No H-bonds generated for 'chain 'I' and resid 71 through 73' Processing helix chain 'I' and resid 77 through 93 Processing helix chain 'I' and resid 99 through 110 Processing helix chain 'I' and resid 134 through 153 Processing helix chain 'I' and resid 160 through 173 Processing helix chain 'I' and resid 179 through 194 Processing helix chain 'J' and resid 17 through 30 Processing helix chain 'J' and resid 38 through 41 No H-bonds generated for 'chain 'J' and resid 38 through 41' Processing helix chain 'J' and resid 66 through 71 Processing helix chain 'J' and resid 77 through 87 Processing helix chain 'J' and resid 119 through 130 Processing helix chain 'J' and resid 165 through 180 Processing helix chain 'K' and resid 6 through 20 Processing helix chain 'K' and resid 32 through 43 Processing helix chain 'K' and resid 86 through 93 Processing helix chain 'K' and resid 113 through 119 Processing helix chain 'L' and resid 88 through 93 Processing helix chain 'L' and resid 107 through 116 Processing helix chain 'L' and resid 170 through 178 removed outlier: 3.547A pdb=" N GLN L 178 " --> pdb=" O GLU L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 192 No H-bonds generated for 'chain 'L' and resid 189 through 192' Processing helix chain 'L' and resid 203 through 212 Processing helix chain 'M' and resid 45 through 56 removed outlier: 4.240A pdb=" N GLU M 51 " --> pdb=" O LYS M 48 " (cutoff:3.500A) Proline residue: M 52 - end of helix Processing helix chain 'M' and resid 76 through 97 removed outlier: 3.529A pdb=" N ILE M 91 " --> pdb=" O GLY M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 113 Processing helix chain 'N' and resid 28 through 44 removed outlier: 3.505A pdb=" N GLU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 101 Processing helix chain 'O' and resid 16 through 29 Processing helix chain 'O' and resid 50 through 63 Processing helix chain 'O' and resid 81 through 88 Processing helix chain 'P' and resid 71 through 88 Processing helix chain 'P' and resid 110 through 122 removed outlier: 4.225A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 25 removed outlier: 4.433A pdb=" N TRP Q 24 " --> pdb=" O ARG Q 20 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA Q 25 " --> pdb=" O THR Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 33 Processing helix chain 'Q' and resid 35 through 39 removed outlier: 3.529A pdb=" N LYS Q 39 " --> pdb=" O THR Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 132 through 137 Processing helix chain 'R' and resid 23 through 35 removed outlier: 4.191A pdb=" N LYS R 27 " --> pdb=" O THR R 23 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 49 Processing helix chain 'R' and resid 67 through 77 Processing helix chain 'R' and resid 91 through 96 Processing helix chain 'R' and resid 129 through 134 removed outlier: 3.701A pdb=" N SER R 134 " --> pdb=" O ASP R 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 34 Processing helix chain 'S' and resid 41 through 50 Processing helix chain 'S' and resid 63 through 73 Processing helix chain 'S' and resid 102 through 119 removed outlier: 3.825A pdb=" N ASP S 106 " --> pdb=" O ALA S 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 129 Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 38 through 48 removed outlier: 5.230A pdb=" N ASP T 46 " --> pdb=" O ARG T 42 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE T 47 " --> pdb=" O GLU T 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 42 Processing helix chain 'U' and resid 47 through 56 Processing helix chain 'U' and resid 63 through 66 No H-bonds generated for 'chain 'U' and resid 63 through 66' Processing helix chain 'U' and resid 71 through 78 Processing helix chain 'U' and resid 86 through 104 Processing helix chain 'U' and resid 109 through 131 Processing helix chain 'U' and resid 146 through 149 No H-bonds generated for 'chain 'U' and resid 146 through 149' Processing helix chain 'V' and resid 49 through 52 No H-bonds generated for 'chain 'V' and resid 49 through 52' Processing helix chain 'V' and resid 154 through 156 No H-bonds generated for 'chain 'V' and resid 154 through 156' Processing helix chain 'W' and resid 7 through 18 removed outlier: 4.215A pdb=" N VAL W 17 " --> pdb=" O ALA W 13 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU W 18 " --> pdb=" O ARG W 14 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 38 Processing helix chain 'W' and resid 45 through 60 Processing helix chain 'W' and resid 72 through 82 Processing helix chain 'W' and resid 100 through 109 Processing helix chain 'X' and resid 22 through 27 Processing helix chain 'X' and resid 30 through 36 Processing helix chain 'X' and resid 39 through 47 Processing helix chain 'X' and resid 50 through 66 removed outlier: 3.996A pdb=" N LYS X 54 " --> pdb=" O SER X 50 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER X 55 " --> pdb=" O LYS X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 89 No H-bonds generated for 'chain 'X' and resid 87 through 89' Processing helix chain 'Y' and resid 29 through 31 No H-bonds generated for 'chain 'Y' and resid 29 through 31' Processing helix chain 'Y' and resid 34 through 48 Processing helix chain 'Y' and resid 56 through 59 Processing helix chain 'Y' and resid 64 through 66 No H-bonds generated for 'chain 'Y' and resid 64 through 66' Processing helix chain 'Y' and resid 75 through 89 Processing helix chain 'Y' and resid 95 through 101 Processing helix chain 'Y' and resid 120 through 133 Processing helix chain 'Y' and resid 149 through 167 Processing helix chain 'Z' and resid 26 through 28 No H-bonds generated for 'chain 'Z' and resid 26 through 28' Processing helix chain 'Z' and resid 56 through 61 Processing helix chain 'Z' and resid 64 through 74 Processing helix chain '1' and resid 37 through 47 Processing helix chain '1' and resid 53 through 55 No H-bonds generated for 'chain '1' and resid 53 through 55' Processing helix chain '1' and resid 80 through 86 Processing helix chain '1' and resid 89 through 95 Processing helix chain '1' and resid 108 through 113 Processing helix chain '2' and resid 61 through 68 Processing helix chain '2' and resid 72 through 83 Processing helix chain '3' and resid 48 through 56 Processing helix chain '3' and resid 75 through 80 Processing helix chain '3' and resid 89 through 93 removed outlier: 4.056A pdb=" N ARG 3 93 " --> pdb=" O ARG 3 89 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 89 through 93' Processing helix chain '6' and resid 13 through 17 Processing helix chain '6' and resid 33 through 43 Processing sheet with id= A, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.614A pdb=" N SER B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHE B 100 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 126 through 128 removed outlier: 3.953A pdb=" N HIS B 134 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS B 219 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG B 136 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 28 through 33 removed outlier: 4.194A pdb=" N GLY B 44 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 73 through 76 removed outlier: 6.171A pdb=" N LEU C 120 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL C 76 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE C 122 " --> pdb=" O VAL C 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 144 through 147 removed outlier: 6.676A pdb=" N ILE C 158 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS C 147 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE C 160 " --> pdb=" O CYS C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 37 through 40 removed outlier: 7.060A pdb=" N ILE C 47 " --> pdb=" O TYR C 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 151 through 154 removed outlier: 3.651A pdb=" N GLY D 134 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY D 181 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 70 through 72 Processing sheet with id= I, first strand: chain 'F' and resid 101 through 103 Processing sheet with id= J, first strand: chain 'F' and resid 121 through 125 removed outlier: 3.533A pdb=" N THR F 159 " --> pdb=" O LEU F 173 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU F 171 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ASP F 163 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 146 through 148 removed outlier: 3.508A pdb=" N LEU F 136 " --> pdb=" O ARG F 132 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 181 through 183 Processing sheet with id= M, first strand: chain 'F' and resid 207 through 211 Processing sheet with id= N, first strand: chain 'G' and resid 89 through 91 Processing sheet with id= O, first strand: chain 'G' and resid 94 through 99 removed outlier: 3.846A pdb=" N LYS G 94 " --> pdb=" O PHE G 113 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 170 through 174 Processing sheet with id= Q, first strand: chain 'H' and resid 2 through 7 Processing sheet with id= R, first strand: chain 'H' and resid 35 through 37 removed outlier: 5.757A pdb=" N ARG H 51 " --> pdb=" O LEU H 113 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU H 113 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 72 through 76 Processing sheet with id= T, first strand: chain 'I' and resid 114 through 117 Processing sheet with id= U, first strand: chain 'J' and resid 46 through 51 removed outlier: 6.798A pdb=" N TYR J 91 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE J 62 " --> pdb=" O TYR J 91 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL J 93 " --> pdb=" O ILE J 62 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE J 64 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL J 95 " --> pdb=" O ILE J 64 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 141 through 143 Processing sheet with id= W, first strand: chain 'K' and resid 24 through 27 removed outlier: 3.754A pdb=" N VAL K 62 " --> pdb=" O GLU K 51 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 72 through 74 removed outlier: 6.709A pdb=" N ILE K 103 " --> pdb=" O LEU K 126 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE K 128 " --> pdb=" O HIS K 101 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N HIS K 101 " --> pdb=" O PHE K 128 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 64 through 67 Processing sheet with id= Z, first strand: chain 'L' and resid 197 through 199 removed outlier: 3.680A pdb=" N ASP L 80 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP L 105 " --> pdb=" O ILE L 78 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE L 78 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 42 through 48 removed outlier: 6.372A pdb=" N HIS L 44 " --> pdb=" O ALA L 57 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ALA L 57 " --> pdb=" O HIS L 44 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL L 46 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N TYR L 55 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLY L 48 " --> pdb=" O TYR L 53 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR L 53 " --> pdb=" O GLY L 48 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 7 through 11 Processing sheet with id= AC, first strand: chain 'N' and resid 84 through 87 Processing sheet with id= AD, first strand: chain 'N' and resid 59 through 65 removed outlier: 3.513A pdb=" N THR N 64 " --> pdb=" O ASP N 77 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'O' and resid 66 through 68 Processing sheet with id= AF, first strand: chain 'P' and resid 92 through 98 Processing sheet with id= AG, first strand: chain 'Q' and resid 122 through 124 removed outlier: 6.608A pdb=" N ARG Q 73 " --> pdb=" O VAL Q 54 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS Q 56 " --> pdb=" O CYS Q 71 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N CYS Q 71 " --> pdb=" O LYS Q 56 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA Q 58 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG Q 69 " --> pdb=" O ALA Q 58 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'R' and resid 38 through 40 Processing sheet with id= AI, first strand: chain 'V' and resid 105 through 113 removed outlier: 3.555A pdb=" N ILE V 88 " --> pdb=" O SER V 80 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER V 80 " --> pdb=" O ILE V 88 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG V 90 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL V 78 " --> pdb=" O ARG V 90 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN V 92 " --> pdb=" O GLY V 76 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLY V 76 " --> pdb=" O ASN V 92 " (cutoff:3.500A) removed outlier: 14.056A pdb=" N LEU V 94 " --> pdb=" O LEU V 74 " (cutoff:3.500A) removed outlier: 16.190A pdb=" N LEU V 74 " --> pdb=" O LEU V 94 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY V 129 " --> pdb=" O VAL V 142 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL V 142 " --> pdb=" O GLY V 129 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Y' and resid 104 through 106 Processing sheet with id= AK, first strand: chain 'Z' and resid 32 through 37 Processing sheet with id= AL, first strand: chain '1' and resid 6 through 10 Processing sheet with id= AM, first strand: chain '1' and resid 13 through 15 Processing sheet with id= AN, first strand: chain '3' and resid 20 through 22 Processing sheet with id= AO, first strand: chain '3' and resid 36 through 38 Processing sheet with id= AP, first strand: chain '3' and resid 41 through 43 Processing sheet with id= AQ, first strand: chain '4' and resid 31 through 34 removed outlier: 3.537A pdb=" N SER 4 76 " --> pdb=" O LYS 4 34 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain '5' and resid 53 through 56 removed outlier: 3.623A pdb=" N ALA 5 7 " --> pdb=" O LEU 5 54 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG 5 26 " --> pdb=" O GLU 5 10 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL 5 12 " --> pdb=" O GLN 5 24 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLN 5 24 " --> pdb=" O VAL 5 12 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain '5' and resid 14 through 16 removed outlier: 3.655A pdb=" N GLY 5 14 " --> pdb=" O GLN 5 24 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL 5 22 " --> pdb=" O THR 5 16 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 3030 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1143 hydrogen bonds 1864 hydrogen bond angles 0 basepair planarities 482 basepair parallelities 897 stacking parallelities Total time for adding SS restraints: 46.93 Time building geometry restraints manager: 30.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7756 1.32 - 1.45: 29017 1.45 - 1.57: 33241 1.57 - 1.70: 3343 1.70 - 1.83: 208 Bond restraints: 73565 Sorted by residual: bond pdb=" C1' U A 789 " pdb=" N1 U A 789 " ideal model delta sigma weight residual 1.480 1.587 -0.107 1.50e-02 4.44e+03 5.08e+01 bond pdb=" O3' A A 788 " pdb=" P U A 789 " ideal model delta sigma weight residual 1.607 1.703 -0.096 1.50e-02 4.44e+03 4.11e+01 bond pdb=" CAM 34G A2168 " pdb=" CAX 34G A2168 " ideal model delta sigma weight residual 1.504 1.377 0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C1' A A 788 " pdb=" N9 A A 788 " ideal model delta sigma weight residual 1.475 1.391 0.084 1.50e-02 4.44e+03 3.13e+01 bond pdb=" CAL 34G A2168 " pdb=" CAW 34G A2168 " ideal model delta sigma weight residual 1.505 1.412 0.093 2.00e-02 2.50e+03 2.17e+01 ... (remaining 73560 not shown) Histogram of bond angle deviations from ideal: 93.53 - 101.75: 2313 101.75 - 109.97: 25715 109.97 - 118.18: 39457 118.18 - 126.40: 34605 126.40 - 134.62: 5148 Bond angle restraints: 107238 Sorted by residual: angle pdb=" O3' U A2053 " pdb=" C3' U A2053 " pdb=" C2' U A2053 " ideal model delta sigma weight residual 109.50 126.57 -17.07 1.50e+00 4.44e-01 1.30e+02 angle pdb=" O3' U A1386 " pdb=" C3' U A1386 " pdb=" C2' U A1386 " ideal model delta sigma weight residual 109.50 125.28 -15.78 1.50e+00 4.44e-01 1.11e+02 angle pdb=" O3' G A 465 " pdb=" C3' G A 465 " pdb=" C2' G A 465 " ideal model delta sigma weight residual 109.50 123.81 -14.31 1.50e+00 4.44e-01 9.09e+01 angle pdb=" C3' A A 788 " pdb=" O3' A A 788 " pdb=" P U A 789 " ideal model delta sigma weight residual 120.20 106.69 13.51 1.50e+00 4.44e-01 8.12e+01 angle pdb=" C4' A A1897 " pdb=" C3' A A1897 " pdb=" O3' A A1897 " ideal model delta sigma weight residual 109.40 122.36 -12.96 1.50e+00 4.44e-01 7.46e+01 ... (remaining 107233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 40027 35.91 - 71.82: 3921 71.82 - 107.72: 437 107.72 - 143.63: 20 143.63 - 179.54: 54 Dihedral angle restraints: 44459 sinusoidal: 32584 harmonic: 11875 Sorted by residual: dihedral pdb=" CA SER K 76 " pdb=" C SER K 76 " pdb=" N PRO K 77 " pdb=" CA PRO K 77 " ideal model delta harmonic sigma weight residual -180.00 -128.59 -51.41 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" O4' C A1702 " pdb=" C1' C A1702 " pdb=" N1 C A1702 " pdb=" C2 C A1702 " ideal model delta sinusoidal sigma weight residual 200.00 22.80 177.20 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1069 " pdb=" C1' C A1069 " pdb=" N1 C A1069 " pdb=" C2 C A1069 " ideal model delta sinusoidal sigma weight residual 200.00 24.67 175.33 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 44456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 11543 0.160 - 0.319: 1806 0.319 - 0.479: 70 0.479 - 0.639: 11 0.639 - 0.798: 4 Chirality restraints: 13434 Sorted by residual: chirality pdb=" C3' U A2053 " pdb=" C4' U A2053 " pdb=" O3' U A2053 " pdb=" C2' U A2053 " both_signs ideal model delta sigma weight residual False -2.74 -1.95 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" C3' U A1386 " pdb=" C4' U A1386 " pdb=" O3' U A1386 " pdb=" C2' U A1386 " both_signs ideal model delta sigma weight residual False -2.74 -2.06 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" C3' A A 105 " pdb=" C4' A A 105 " pdb=" O3' A A 105 " pdb=" C2' A A 105 " both_signs ideal model delta sigma weight residual False -2.74 -2.06 -0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 13431 not shown) Planarity restraints: 7296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 76 " -0.101 5.00e-02 4.00e+02 1.53e-01 3.77e+01 pdb=" N PRO K 77 " 0.265 5.00e-02 4.00e+02 pdb=" CA PRO K 77 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO K 77 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A 427 " 0.060 2.00e-02 2.50e+03 2.71e-02 2.02e+01 pdb=" N9 A A 427 " -0.062 2.00e-02 2.50e+03 pdb=" C8 A A 427 " -0.007 2.00e-02 2.50e+03 pdb=" N7 A A 427 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A 427 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A A 427 " 0.013 2.00e-02 2.50e+03 pdb=" N6 A A 427 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A A 427 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 427 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A A 427 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A A 427 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1209 " -0.063 2.00e-02 2.50e+03 2.51e-02 1.90e+01 pdb=" N9 G A1209 " 0.047 2.00e-02 2.50e+03 pdb=" C8 G A1209 " 0.013 2.00e-02 2.50e+03 pdb=" N7 G A1209 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G A1209 " 0.007 2.00e-02 2.50e+03 pdb=" C6 G A1209 " -0.020 2.00e-02 2.50e+03 pdb=" O6 G A1209 " -0.019 2.00e-02 2.50e+03 pdb=" N1 G A1209 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A1209 " 0.009 2.00e-02 2.50e+03 pdb=" N2 G A1209 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G A1209 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G A1209 " 0.017 2.00e-02 2.50e+03 ... (remaining 7293 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 94 2.35 - 2.99: 32162 2.99 - 3.63: 117008 3.63 - 4.26: 192117 4.26 - 4.90: 271627 Nonbonded interactions: 613008 Sorted by model distance: nonbonded pdb=" OP1 A A 169 " pdb="MG MG A2155 " model vdw 1.715 2.170 nonbonded pdb=" O ILE S 35 " pdb=" CG1 ILE S 38 " model vdw 1.757 3.440 nonbonded pdb=" OP2 A A 998 " pdb="MG MG A2140 " model vdw 1.822 2.170 nonbonded pdb=" O2 C A 759 " pdb=" C2 A A 788 " model vdw 1.841 3.340 nonbonded pdb=" O2' A A1447 " pdb=" OP2 U A1448 " model vdw 1.847 2.440 ... (remaining 613003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 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: 0.050 Extract box with map and model: 12.220 Check model and map are aligned: 0.730 Set scattering table: 0.470 Process input model: 189.740 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.170 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:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 209.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5417 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.127 73565 Z= 0.495 Angle : 1.394 17.070 107238 Z= 0.941 Chirality : 0.103 0.798 13434 Planarity : 0.007 0.153 7296 Dihedral : 23.366 179.539 36776 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 4.16 % Allowed : 10.46 % Favored : 85.38 % Rotamer: Outliers : 15.41 % Allowed : 15.77 % Favored : 68.83 % Cbeta Deviations : 1.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.12), residues: 4014 helix: 1.04 (0.11), residues: 1421 sheet: -2.97 (0.17), residues: 597 loop : -3.42 (0.12), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP O 72 HIS 0.015 0.002 HIS K 101 PHE 0.038 0.003 PHE L 65 TYR 0.032 0.003 TYR G 234 ARG 0.012 0.001 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1645 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 556 poor density : 1089 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 556 outliers final: 109 residues processed: 1451 average time/residue: 0.7916 time to fit residues: 1827.9269 Evaluate side-chains 756 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 647 time to evaluate : 3.655 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 0 residues processed: 109 average time/residue: 0.5921 time to fit residues: 119.4437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 473 optimal weight: 9.9990 chunk 425 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 439 optimal weight: 8.9990 chunk 170 optimal weight: 20.0000 chunk 267 optimal weight: 0.7980 chunk 327 optimal weight: 5.9990 chunk 509 optimal weight: 0.5980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN C 131 GLN D 13 ASN E 38 ASN E 110 GLN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN F 74 ASN F 151 HIS ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS H 11 ASN I 74 ASN I 194 ASN J 107 ASN K 39 GLN K 70 ASN L 21 HIS L 88 ASN M 36 ASN M 75 GLN N 27 ASN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 ASN U 69 ASN U 101 HIS U 105 ASN V 16 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 109 ASN W 31 ASN W 48 ASN W 62 GLN X 82 ASN Y 48 HIS Y 168 ASN 1 15 ASN 1 52 ASN 2 81 HIS 4 7 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 73565 Z= 0.295 Angle : 0.847 13.435 107238 Z= 0.426 Chirality : 0.044 0.367 13434 Planarity : 0.007 0.150 7296 Dihedral : 22.372 179.179 28159 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 1.64 % Allowed : 8.42 % Favored : 89.94 % Rotamer: Outliers : 6.04 % Allowed : 21.95 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 4014 helix: 1.75 (0.14), residues: 1399 sheet: -2.19 (0.19), residues: 566 loop : -2.86 (0.12), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP O 72 HIS 0.011 0.002 HIS D 126 PHE 0.023 0.003 PHE Z 80 TYR 0.025 0.002 TYR Y 76 ARG 0.035 0.001 ARG N 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 838 time to evaluate : 3.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 218 outliers final: 87 residues processed: 971 average time/residue: 0.7514 time to fit residues: 1209.9185 Evaluate side-chains 701 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 614 time to evaluate : 3.608 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 0.5692 time to fit residues: 96.6262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 283 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 424 optimal weight: 0.8980 chunk 346 optimal weight: 5.9990 chunk 140 optimal weight: 40.0000 chunk 510 optimal weight: 2.9990 chunk 551 optimal weight: 3.9990 chunk 454 optimal weight: 3.9990 chunk 506 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 409 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 HIS H 59 GLN I 74 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 ASN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 ASN M 36 ASN M 78 GLN Q 33 HIS ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 GLN T 24 ASN U 105 ASN V 16 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 ASN ** W 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 128 GLN 2 81 HIS 3 14 ASN 4 7 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.6515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 73565 Z= 0.222 Angle : 0.683 11.623 107238 Z= 0.349 Chirality : 0.039 0.419 13434 Planarity : 0.006 0.146 7296 Dihedral : 22.081 179.604 28159 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 1.47 % Allowed : 8.97 % Favored : 89.56 % Rotamer: Outliers : 4.07 % Allowed : 24.24 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 4014 helix: 1.51 (0.14), residues: 1407 sheet: -1.69 (0.20), residues: 558 loop : -2.67 (0.12), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP F 18 HIS 0.009 0.001 HIS P 43 PHE 0.023 0.002 PHE D 24 TYR 0.024 0.002 TYR Z 73 ARG 0.014 0.001 ARG S 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 769 time to evaluate : 3.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 147 outliers final: 64 residues processed: 858 average time/residue: 0.7139 time to fit residues: 1016.8372 Evaluate side-chains 706 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 642 time to evaluate : 3.683 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.5092 time to fit residues: 66.5906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 504 optimal weight: 0.8980 chunk 383 optimal weight: 30.0000 chunk 264 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 342 optimal weight: 5.9990 chunk 512 optimal weight: 7.9990 chunk 542 optimal weight: 20.0000 chunk 267 optimal weight: 8.9990 chunk 485 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN C 131 GLN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN F 187 HIS F 201 ASN F 215 ASN ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 HIS ** H 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN I 101 GLN I 108 GLN I 194 ASN ** P 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 ASN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 137 HIS V 16 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 66 ASN ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 ASN Y 153 ASN Z 61 ASN 2 81 HIS 3 71 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.9574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 73565 Z= 0.356 Angle : 0.822 13.931 107238 Z= 0.417 Chirality : 0.045 0.371 13434 Planarity : 0.007 0.147 7296 Dihedral : 22.306 179.866 28159 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 1.42 % Allowed : 9.42 % Favored : 89.16 % Rotamer: Outliers : 5.13 % Allowed : 25.82 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.12), residues: 4014 helix: 0.31 (0.13), residues: 1394 sheet: -1.69 (0.19), residues: 616 loop : -2.68 (0.12), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP O 72 HIS 0.015 0.003 HIS P 43 PHE 0.048 0.003 PHE E 114 TYR 0.028 0.003 TYR W 21 ARG 0.022 0.001 ARG W 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 887 time to evaluate : 3.721 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 outliers start: 185 outliers final: 94 residues processed: 1013 average time/residue: 0.7409 time to fit residues: 1235.3292 Evaluate side-chains 770 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 676 time to evaluate : 3.751 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 0 residues processed: 94 average time/residue: 0.5230 time to fit residues: 98.1341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 451 optimal weight: 0.5980 chunk 307 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 403 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 462 optimal weight: 9.9990 chunk 374 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 486 optimal weight: 10.0000 chunk 136 optimal weight: 40.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS B 208 GLN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 ASN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN G 228 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN I 156 ASN J 107 ASN ** K 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 ASN P 38 ASN P 43 HIS ** Q 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN Q 79 ASN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 ASN Y 128 GLN Z 33 GLN 2 81 HIS 4 40 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 1.0382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 73565 Z= 0.330 Angle : 0.744 11.332 107238 Z= 0.376 Chirality : 0.042 0.436 13434 Planarity : 0.006 0.149 7296 Dihedral : 22.234 179.063 28159 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 1.40 % Allowed : 8.94 % Favored : 89.66 % Rotamer: Outliers : 4.13 % Allowed : 27.29 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.12), residues: 4014 helix: 0.25 (0.13), residues: 1388 sheet: -1.61 (0.19), residues: 610 loop : -2.53 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 255 HIS 0.012 0.002 HIS P 43 PHE 0.029 0.002 PHE 4 77 TYR 0.026 0.002 TYR T 12 ARG 0.014 0.001 ARG S 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 789 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 149 outliers final: 62 residues processed: 880 average time/residue: 0.7359 time to fit residues: 1066.3247 Evaluate side-chains 754 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 692 time to evaluate : 3.685 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.5644 time to fit residues: 68.7185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 182 optimal weight: 20.0000 chunk 488 optimal weight: 2.9990 chunk 107 optimal weight: 40.0000 chunk 318 optimal weight: 0.0670 chunk 133 optimal weight: 40.0000 chunk 542 optimal weight: 4.9990 chunk 450 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 284 optimal weight: 9.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 HIS ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN J 164 ASN K 56 HIS P 94 HIS ** Q 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN Q 79 ASN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 HIS ** Y 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 35 ASN Z 60 GLN ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS ** 3 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 1.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 73565 Z= 0.215 Angle : 0.651 11.116 107238 Z= 0.331 Chirality : 0.038 0.369 13434 Planarity : 0.005 0.144 7296 Dihedral : 22.089 179.526 28159 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 1.30 % Allowed : 8.05 % Favored : 90.66 % Rotamer: Outliers : 2.74 % Allowed : 28.18 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -1.86 (0.13), residues: 4014 helix: 0.46 (0.13), residues: 1397 sheet: -1.48 (0.20), residues: 608 loop : -2.47 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 255 HIS 0.008 0.001 HIS Z 57 PHE 0.019 0.002 PHE Z 80 TYR 0.021 0.002 TYR Y 76 ARG 0.010 0.001 ARG N 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 769 time to evaluate : 3.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 49 residues processed: 822 average time/residue: 0.7358 time to fit residues: 1000.8221 Evaluate side-chains 750 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 701 time to evaluate : 4.317 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.6117 time to fit residues: 59.9507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 523 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 chunk 396 optimal weight: 0.2980 chunk 307 optimal weight: 5.9990 chunk 456 optimal weight: 1.9990 chunk 303 optimal weight: 0.0270 chunk 540 optimal weight: 10.0000 chunk 338 optimal weight: 20.0000 chunk 329 optimal weight: 20.0000 chunk 249 optimal weight: 10.0000 overall best weight: 1.8644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 HIS ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN D 126 HIS ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 112 HIS F 151 HIS F 254 ASN G 228 ASN G 246 ASN I 34 GLN I 74 ASN I 101 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN J 164 ASN P 38 ASN ** Q 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN T 14 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 101 GLN Y 139 ASN ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS ** 3 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 1.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 73565 Z= 0.167 Angle : 0.613 12.829 107238 Z= 0.312 Chirality : 0.036 0.361 13434 Planarity : 0.005 0.141 7296 Dihedral : 21.956 179.734 28159 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 1.25 % Allowed : 7.75 % Favored : 91.01 % Rotamer: Outliers : 2.08 % Allowed : 29.07 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -1.66 (0.13), residues: 4014 helix: 0.66 (0.14), residues: 1398 sheet: -1.33 (0.20), residues: 603 loop : -2.40 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP S 84 HIS 0.011 0.001 HIS F 36 PHE 0.026 0.002 PHE G 258 TYR 0.022 0.001 TYR M 94 ARG 0.008 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 736 time to evaluate : 3.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 35 residues processed: 774 average time/residue: 0.7395 time to fit residues: 946.2179 Evaluate side-chains 720 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 685 time to evaluate : 3.713 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.6008 time to fit residues: 42.2706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 334 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 322 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 106 optimal weight: 40.0000 chunk 104 optimal weight: 30.0000 chunk 343 optimal weight: 10.0000 chunk 368 optimal weight: 0.0970 chunk 267 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 425 optimal weight: 7.9990 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN C 164 ASN D 22 ASN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN G 228 ASN G 246 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN R 95 HIS S 71 HIS T 14 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS ** 3 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 1.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 73565 Z= 0.311 Angle : 0.721 12.031 107238 Z= 0.363 Chirality : 0.041 0.395 13434 Planarity : 0.006 0.145 7296 Dihedral : 22.092 179.463 28159 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 1.25 % Allowed : 9.02 % Favored : 89.74 % Rotamer: Outliers : 2.05 % Allowed : 29.34 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.13), residues: 4014 helix: 0.33 (0.13), residues: 1400 sheet: -1.47 (0.20), residues: 620 loop : -2.46 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 255 HIS 0.011 0.002 HIS 4 17 PHE 0.029 0.002 PHE Q 107 TYR 0.027 0.002 TYR Y 76 ARG 0.011 0.001 ARG N 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 735 time to evaluate : 4.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 44 residues processed: 778 average time/residue: 0.7471 time to fit residues: 959.6030 Evaluate side-chains 725 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 681 time to evaluate : 3.754 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.5284 time to fit residues: 48.7428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 491 optimal weight: 8.9990 chunk 518 optimal weight: 3.9990 chunk 472 optimal weight: 2.9990 chunk 503 optimal weight: 9.9990 chunk 517 optimal weight: 7.9990 chunk 303 optimal weight: 0.0770 chunk 219 optimal weight: 5.9990 chunk 395 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 455 optimal weight: 5.9990 chunk 476 optimal weight: 6.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN I 101 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 GLN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 HIS ** Q 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN T 14 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 1.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 73565 Z= 0.230 Angle : 0.656 11.974 107238 Z= 0.332 Chirality : 0.038 0.289 13434 Planarity : 0.005 0.145 7296 Dihedral : 21.998 179.324 28159 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 1.22 % Allowed : 8.47 % Favored : 90.31 % Rotamer: Outliers : 1.41 % Allowed : 29.93 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -1.82 (0.13), residues: 4014 helix: 0.40 (0.13), residues: 1408 sheet: -1.44 (0.20), residues: 603 loop : -2.39 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 255 HIS 0.008 0.001 HIS F 36 PHE 0.026 0.002 PHE S 85 TYR 0.022 0.002 TYR G 155 ARG 0.011 0.001 ARG S 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 745 time to evaluate : 3.725 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 outliers start: 51 outliers final: 22 residues processed: 768 average time/residue: 0.7600 time to fit residues: 955.5473 Evaluate side-chains 713 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 691 time to evaluate : 4.027 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.5881 time to fit residues: 28.2071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 502 optimal weight: 9.9990 chunk 330 optimal weight: 0.9980 chunk 532 optimal weight: 0.9980 chunk 325 optimal weight: 4.9990 chunk 252 optimal weight: 0.4980 chunk 370 optimal weight: 0.0980 chunk 558 optimal weight: 40.0000 chunk 514 optimal weight: 9.9990 chunk 445 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 343 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 HIS F 96 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 GLN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 HIS Q 33 HIS Q 63 GLN Q 75 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 HIS ** Y 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 63 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 1.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 73565 Z= 0.149 Angle : 0.607 12.316 107238 Z= 0.307 Chirality : 0.035 0.258 13434 Planarity : 0.005 0.141 7296 Dihedral : 21.790 179.439 28159 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 1.15 % Allowed : 7.45 % Favored : 91.41 % Rotamer: Outliers : 0.72 % Allowed : 31.23 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 4014 helix: 0.65 (0.14), residues: 1399 sheet: -1.24 (0.20), residues: 615 loop : -2.32 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 255 HIS 0.010 0.001 HIS Q 33 PHE 0.028 0.001 PHE S 85 TYR 0.020 0.001 TYR 1 90 ARG 0.020 0.001 ARG D 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 795 time to evaluate : 3.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 805 average time/residue: 0.7725 time to fit residues: 1019.5642 Evaluate side-chains 709 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 699 time to evaluate : 3.650 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5075 time to fit residues: 14.2967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 272 optimal weight: 0.0770 chunk 353 optimal weight: 9.9990 chunk 474 optimal weight: 0.0000 chunk 136 optimal weight: 40.0000 chunk 410 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 445 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 457 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 overall best weight: 0.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 HIS ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN G 228 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN O 43 HIS O 50 ASN Q 33 HIS Q 75 GLN T 14 GLN T 35 ASN U 45 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 15 ASN ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 7 ASN 4 40 GLN 6 41 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.182365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.154756 restraints weight = 123961.195| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.15 r_work: 0.3753 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 1.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 73565 Z= 0.147 Angle : 0.591 13.162 107238 Z= 0.298 Chirality : 0.034 0.306 13434 Planarity : 0.005 0.140 7296 Dihedral : 21.696 179.707 28159 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 1.15 % Allowed : 7.35 % Favored : 91.50 % Rotamer: Outliers : 0.58 % Allowed : 32.00 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -1.51 (0.13), residues: 4014 helix: 0.68 (0.14), residues: 1414 sheet: -1.17 (0.20), residues: 599 loop : -2.27 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP G 255 HIS 0.008 0.001 HIS S 137 PHE 0.027 0.001 PHE G 258 TYR 0.022 0.002 TYR T 12 ARG 0.017 0.001 ARG K 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17390.81 seconds wall clock time: 306 minutes 53.21 seconds (18413.21 seconds total)