Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 01:03:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/10_2023/3j7a_2660_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/10_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_2660/10_2023/3j7a_2660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/10_2023/3j7a_2660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/10_2023/3j7a_2660_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/10_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-1.21rc1-5097/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: 29.33, per 1000 atoms: 0.43 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: 31.20 Conformation dependent library (CDL) restraints added in 3.7 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: 26.04 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: 49.80 Time building geometry restraints manager: 33.61 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: 38428 35.91 - 71.82: 2275 71.82 - 107.72: 170 107.72 - 143.63: 20 143.63 - 179.54: 54 Dihedral angle restraints: 40947 sinusoidal: 29072 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 40944 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: 5.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 12.720 Check model and map are aligned: 0.770 Set scattering table: 0.490 Process input model: 200.180 Find NCS groups from input model: 1.400 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 223.500 ------------------------------------------------------------------------------- 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 : 19.810 179.539 33264 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 *********************** 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 : 3.578 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: 0.8512 time to fit residues: 1991.7500 Evaluate side-chains 756 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 647 time to evaluate : 3.603 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 0 residues processed: 109 average time/residue: 0.6163 time to fit residues: 124.9965 ------------------------------------------------------------------------------- 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 F 13 ASN F 74 ASN ** F 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 3 14 ASN 4 7 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 73565 Z= 0.299 Angle : 0.834 13.361 107238 Z= 0.423 Chirality : 0.044 0.361 13434 Planarity : 0.007 0.149 7296 Dihedral : 17.187 179.341 24647 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 1.64 % Allowed : 8.94 % Favored : 89.41 % Rotamer: Outliers : 5.68 % Allowed : 22.17 % Favored : 72.15 % 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: -1.54 (0.13), residues: 4014 helix: 1.84 (0.14), residues: 1402 sheet: -2.27 (0.19), residues: 571 loop : -2.88 (0.12), residues: 2041 *********************** 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 1026 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 821 time to evaluate : 3.631 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 outliers start: 205 outliers final: 89 residues processed: 944 average time/residue: 0.7224 time to fit residues: 1126.9161 Evaluate side-chains 708 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 619 time to evaluate : 3.747 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 0.5301 time to fit residues: 94.0493 ------------------------------------------------------------------------------- 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: 7.9990 chunk 346 optimal weight: 5.9990 chunk 140 optimal weight: 40.0000 chunk 510 optimal weight: 0.9990 chunk 551 optimal weight: 0.2980 chunk 454 optimal weight: 2.9990 chunk 506 optimal weight: 7.9990 chunk 173 optimal weight: 0.9980 chunk 409 optimal weight: 20.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 GLN D 13 ASN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN F 215 ASN G 65 HIS G 86 HIS H 176 GLN I 74 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 ASN K 101 HIS ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 ASN Q 33 HIS S 87 ASN S 104 GLN T 24 ASN U 105 ASN V 16 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 ASN ** V 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 153 ASN 2 81 HIS 4 7 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 73565 Z= 0.212 Angle : 0.680 11.208 107238 Z= 0.348 Chirality : 0.039 0.397 13434 Planarity : 0.006 0.144 7296 Dihedral : 16.690 179.419 24647 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 1.49 % Allowed : 8.84 % Favored : 89.66 % Rotamer: Outliers : 4.54 % Allowed : 23.88 % Favored : 71.57 % 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: -1.39 (0.13), residues: 4014 helix: 1.55 (0.14), residues: 1418 sheet: -1.75 (0.20), residues: 568 loop : -2.64 (0.12), residues: 2028 *********************** 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 934 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 770 time to evaluate : 3.737 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: 164 outliers final: 63 residues processed: 868 average time/residue: 0.7125 time to fit residues: 1028.0617 Evaluate side-chains 705 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 642 time to evaluate : 3.723 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.5605 time to fit residues: 69.7748 ------------------------------------------------------------------------------- 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: 10.0000 chunk 383 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 342 optimal weight: 9.9990 chunk 512 optimal weight: 8.9990 chunk 542 optimal weight: 20.0000 chunk 267 optimal weight: 0.9980 chunk 485 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 overall best weight: 7.1988 ------------------------------------------------------------------------------- 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 ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 131 GLN C 140 ASN C 155 HIS ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS F 13 ASN F 187 HIS G 122 HIS G 221 ASN ** H 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN I 48 GLN I 101 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 GLN Q 33 HIS S 137 HIS U 45 GLN V 16 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 66 ASN W 31 ASN Z 61 ASN 2 81 HIS 3 71 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.9901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 73565 Z= 0.409 Angle : 0.905 19.835 107238 Z= 0.457 Chirality : 0.048 0.380 13434 Planarity : 0.008 0.149 7296 Dihedral : 17.412 178.966 24647 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 1.47 % Allowed : 9.64 % Favored : 88.89 % Rotamer: Outliers : 5.96 % Allowed : 24.94 % Favored : 69.11 % 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: -2.33 (0.12), residues: 4014 helix: 0.01 (0.13), residues: 1398 sheet: -1.76 (0.19), residues: 633 loop : -2.70 (0.12), residues: 1983 *********************** 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 1127 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 912 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 215 outliers final: 85 residues processed: 1046 average time/residue: 0.7698 time to fit residues: 1328.9954 Evaluate side-chains 794 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 709 time to evaluate : 3.726 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 0 residues processed: 85 average time/residue: 0.5509 time to fit residues: 93.3140 ------------------------------------------------------------------------------- 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: 3.9990 chunk 307 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 403 optimal weight: 7.9990 chunk 223 optimal weight: 8.9990 chunk 462 optimal weight: 4.9990 chunk 374 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 chunk 486 optimal weight: 8.9990 chunk 136 optimal weight: 40.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 208 GLN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 ASN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 HIS G 158 ASN G 221 ASN H 13 GLN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN ** I 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 ASN K 39 GLN K 56 HIS ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN P 38 ASN ** Q 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN Q 79 ASN R 95 HIS ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 GLN Z 60 GLN 2 81 HIS 4 40 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 1.0329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 73565 Z= 0.268 Angle : 0.696 11.526 107238 Z= 0.354 Chirality : 0.040 0.389 13434 Planarity : 0.006 0.146 7296 Dihedral : 16.890 179.990 24647 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 1.37 % Allowed : 8.25 % Favored : 90.38 % Rotamer: Outliers : 3.69 % Allowed : 27.79 % Favored : 68.52 % 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: -1.99 (0.12), residues: 4014 helix: 0.33 (0.13), residues: 1391 sheet: -1.49 (0.19), residues: 605 loop : -2.55 (0.13), residues: 2018 *********************** 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 916 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 783 time to evaluate : 3.747 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 outliers start: 133 outliers final: 61 residues processed: 872 average time/residue: 0.7292 time to fit residues: 1056.0196 Evaluate side-chains 752 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 691 time to evaluate : 3.690 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.5870 time to fit residues: 69.1257 ------------------------------------------------------------------------------- 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: 9.9990 chunk 488 optimal weight: 20.0000 chunk 107 optimal weight: 50.0000 chunk 318 optimal weight: 0.9980 chunk 133 optimal weight: 40.0000 chunk 542 optimal weight: 10.0000 chunk 450 optimal weight: 4.9990 chunk 251 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 284 optimal weight: 30.0000 overall best weight: 6.7988 ------------------------------------------------------------------------------- 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** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 112 HIS G 228 ASN ** H 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN I 74 ASN I 101 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN J 164 ASN K 15 ASN L 88 ASN L 175 GLN ** M 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 ASN T 8 HIS ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 ASN W 56 HIS Y 113 ASN ** Y 139 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** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 1.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 73565 Z= 0.367 Angle : 0.789 14.567 107238 Z= 0.399 Chirality : 0.044 0.398 13434 Planarity : 0.006 0.147 7296 Dihedral : 17.136 179.157 24647 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 1.37 % Allowed : 9.57 % Favored : 89.06 % Rotamer: Outliers : 4.10 % Allowed : 28.37 % Favored : 67.53 % 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: -2.26 (0.12), residues: 4014 helix: -0.07 (0.13), residues: 1403 sheet: -1.65 (0.19), residues: 622 loop : -2.58 (0.13), residues: 1989 *********************** 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 926 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 778 time to evaluate : 3.731 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: 148 outliers final: 74 residues processed: 862 average time/residue: 0.7310 time to fit residues: 1046.6920 Evaluate side-chains 773 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 699 time to evaluate : 3.678 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.5323 time to fit residues: 78.5507 ------------------------------------------------------------------------------- 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: 0.9980 chunk 61 optimal weight: 10.0000 chunk 309 optimal weight: 0.3980 chunk 396 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 chunk 456 optimal weight: 1.9990 chunk 303 optimal weight: 9.9990 chunk 540 optimal weight: 7.9990 chunk 338 optimal weight: 9.9990 chunk 329 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 B 200 GLN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN H 10 ASN H 13 GLN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN I 74 ASN I 101 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN M 36 ASN M 75 GLN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 71 HIS T 35 ASN ** 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** Y 139 ASN ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS 3 25 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 1.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 73565 Z= 0.183 Angle : 0.633 9.315 107238 Z= 0.323 Chirality : 0.037 0.357 13434 Planarity : 0.005 0.142 7296 Dihedral : 16.698 179.721 24647 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 1.32 % Allowed : 7.45 % Favored : 91.23 % Rotamer: Outliers : 2.08 % Allowed : 29.54 % Favored : 68.38 % 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: 0.41 (0.13), residues: 1404 sheet: -1.39 (0.20), residues: 610 loop : -2.47 (0.13), residues: 2000 *********************** 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 872 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 797 time to evaluate : 5.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 32 residues processed: 841 average time/residue: 0.7461 time to fit residues: 1042.5664 Evaluate side-chains 739 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 707 time to evaluate : 4.155 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.5542 time to fit residues: 38.7920 ------------------------------------------------------------------------------- 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: 9.9990 chunk 322 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 106 optimal weight: 40.0000 chunk 104 optimal weight: 30.0000 chunk 343 optimal weight: 1.9990 chunk 368 optimal weight: 20.0000 chunk 267 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 425 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 201 ASN F 215 ASN G 120 ASN H 10 ASN H 13 GLN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN I 101 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN L 88 ASN ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS 4 7 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 1.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 73565 Z= 0.362 Angle : 0.768 12.710 107238 Z= 0.387 Chirality : 0.043 0.343 13434 Planarity : 0.006 0.145 7296 Dihedral : 17.009 178.898 24647 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 1.25 % Allowed : 9.62 % Favored : 89.14 % Rotamer: Outliers : 2.94 % Allowed : 29.84 % Favored : 67.22 % 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: -2.20 (0.12), residues: 4014 helix: -0.10 (0.13), residues: 1420 sheet: -1.55 (0.20), residues: 613 loop : -2.51 (0.13), residues: 1981 *********************** 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 851 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 745 time to evaluate : 3.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 66 residues processed: 800 average time/residue: 0.7311 time to fit residues: 966.0936 Evaluate side-chains 760 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 694 time to evaluate : 3.671 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.5167 time to fit residues: 69.3663 ------------------------------------------------------------------------------- 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: 0.0870 chunk 518 optimal weight: 0.8980 chunk 472 optimal weight: 10.0000 chunk 503 optimal weight: 2.9990 chunk 517 optimal weight: 4.9990 chunk 303 optimal weight: 50.0000 chunk 219 optimal weight: 0.9990 chunk 395 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 455 optimal weight: 7.9990 chunk 476 optimal weight: 7.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- 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 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 142 HIS ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN M 84 GLN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN T 35 ASN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 HIS ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS ** 3 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 63 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 1.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 73565 Z= 0.183 Angle : 0.634 17.093 107238 Z= 0.323 Chirality : 0.037 0.294 13434 Planarity : 0.005 0.141 7296 Dihedral : 16.624 179.864 24647 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 1.25 % Allowed : 7.90 % Favored : 90.86 % Rotamer: Outliers : 1.08 % Allowed : 30.40 % Favored : 68.52 % 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: -1.91 (0.13), residues: 4014 helix: 0.26 (0.13), residues: 1416 sheet: -1.41 (0.20), residues: 603 loop : -2.43 (0.13), residues: 1995 *********************** 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 778 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 739 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 outliers start: 39 outliers final: 17 residues processed: 758 average time/residue: 0.7364 time to fit residues: 919.7371 Evaluate side-chains 701 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 684 time to evaluate : 3.643 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.5565 time to fit residues: 21.9175 ------------------------------------------------------------------------------- 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: 8.9990 chunk 330 optimal weight: 10.0000 chunk 532 optimal weight: 0.8980 chunk 325 optimal weight: 20.0000 chunk 252 optimal weight: 5.9990 chunk 370 optimal weight: 4.9990 chunk 558 optimal weight: 40.0000 chunk 514 optimal weight: 6.9990 chunk 445 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 343 optimal weight: 0.0000 overall best weight: 2.9790 ------------------------------------------------------------------------------- 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 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN F 215 ASN G 228 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 HIS I 101 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 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 ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 66 ASN ** V 141 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 1.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 73565 Z= 0.208 Angle : 0.644 16.927 107238 Z= 0.327 Chirality : 0.037 0.279 13434 Planarity : 0.006 0.143 7296 Dihedral : 16.554 179.713 24647 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 1.25 % Allowed : 8.47 % Favored : 90.28 % Rotamer: Outliers : 0.72 % Allowed : 31.48 % Favored : 67.80 % 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: 0.32 (0.13), residues: 1416 sheet: -1.35 (0.20), residues: 618 loop : -2.44 (0.13), residues: 1980 ********************** 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 734 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 708 time to evaluate : 4.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 22 residues processed: 716 average time/residue: 0.7440 time to fit residues: 879.3650 Evaluate side-chains 688 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 666 time to evaluate : 3.702 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.5570 time to fit residues: 27.8512 ------------------------------------------------------------------------------- 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: 9.9990 chunk 353 optimal weight: 9.9990 chunk 474 optimal weight: 10.0000 chunk 136 optimal weight: 40.0000 chunk 410 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 445 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 457 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 105 GLN ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 HIS ** L 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 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** V 66 ASN ** W 31 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.172193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.148867 restraints weight = 121004.510| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.05 r_work: 0.3674 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 1.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 73565 Z= 0.330 Angle : 0.733 17.112 107238 Z= 0.371 Chirality : 0.041 0.330 13434 Planarity : 0.006 0.146 7296 Dihedral : 16.830 179.897 24647 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 1.20 % Allowed : 9.39 % Favored : 89.41 % Rotamer: Outliers : 0.89 % Allowed : 31.01 % Favored : 68.11 % 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: -2.11 (0.13), residues: 4014 helix: 0.03 (0.13), residues: 1407 sheet: -1.46 (0.20), residues: 623 loop : -2.52 (0.13), residues: 1984 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17179.20 seconds wall clock time: 303 minutes 27.38 seconds (18207.38 seconds total)