Starting phenix.real_space_refine on Thu Dec 14 14:02:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j81_2763/12_2023/3j81_2763.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j81_2763/12_2023/3j81_2763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j81_2763/12_2023/3j81_2763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j81_2763/12_2023/3j81_2763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j81_2763/12_2023/3j81_2763.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j81_2763/12_2023/3j81_2763.pdb" } resolution = 4.0 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= 0.023 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 3 6.06 5 P 1876 5.49 5 Mg 81 5.21 5 S 97 5.16 5 C 45426 2.51 5 N 15207 2.21 5 O 21070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 12": "OE1" <-> "OE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 50": "OE1" <-> "OE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "I GLU 141": "OE1" <-> "OE2" Residue "I GLU 154": "OE1" <-> "OE2" Residue "I GLU 189": "OE1" <-> "OE2" Residue "J GLU 72": "OE1" <-> "OE2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J GLU 153": "OE1" <-> "OE2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "L GLU 50": "OE1" <-> "OE2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "M GLU 40": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M GLU 74": "OE1" <-> "OE2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N GLU 119": "OE1" <-> "OE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P GLU 118": "OE1" <-> "OE2" Residue "P ARG 130": "NH1" <-> "NH2" Residue "Q GLU 125": "OE1" <-> "OE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "S GLU 114": "OE1" <-> "OE2" Residue "T GLU 143": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "U GLU 35": "OE1" <-> "OE2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "U GLU 115": "OE1" <-> "OE2" Residue "V GLU 64": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W GLU 114": "OE1" <-> "OE2" Residue "X GLU 101": "OE1" <-> "OE2" Residue "Y GLU 42": "OE1" <-> "OE2" Residue "Y GLU 86": "OE1" <-> "OE2" Residue "Z GLU 86": "OE1" <-> "OE2" Residue "a ARG 42": "NH1" <-> "NH2" Residue "a TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 15": "OE1" <-> "OE2" Residue "c GLU 31": "OE1" <-> "OE2" Residue "c PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 58": "OE1" <-> "OE2" Residue "c GLU 62": "OE1" <-> "OE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 246": "OE1" <-> "OE2" Residue "e GLU 22": "OE1" <-> "OE2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ARG 14": "NH1" <-> "NH2" Residue "i GLU 30": "OE1" <-> "OE2" Residue "i GLU 31": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 99": "OE1" <-> "OE2" Residue "j GLU 10": "OE1" <-> "OE2" Residue "j GLU 29": "OE1" <-> "OE2" Residue "j GLU 43": "OE1" <-> "OE2" Residue "j ARG 53": "NH1" <-> "NH2" Residue "j ARG 54": "NH1" <-> "NH2" Residue "j ARG 64": "NH1" <-> "NH2" Residue "j GLU 79": "OE1" <-> "OE2" Residue "j ARG 88": "NH1" <-> "NH2" Residue "j GLU 100": "OE1" <-> "OE2" Residue "j GLU 125": "OE1" <-> "OE2" Residue "j GLU 143": "OE1" <-> "OE2" Residue "j GLU 152": "OE1" <-> "OE2" Residue "j GLU 159": "OE1" <-> "OE2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m GLU 73": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 83760 Number of models: 1 Model: "" Number of chains: 48 Chain: "2" Number of atoms: 37797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1780, 37797 Classifications: {'RNA': 1780} Modifications used: {'rna2p_pur': 161, 'rna2p_pyr': 164, 'rna3p_pur': 776, 'rna3p_pyr': 679} Link IDs: {'rna2p': 325, 'rna3p': 1454} Chain breaks: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {' G%rna3p_pur:plan2': 5, ' C%rna3p_pyr:plan': 4, ' A%rna3p_pur:plan2': 4, ' U%rna3p_pyr:plan': 1, ' C%rna3p_pyr:plan2': 4, ' G%rna3p_pur:plan': 5, ' A%rna3p_pur:plan': 4} Unresolved non-hydrogen planarities: 161 Chain: "A" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1625 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 16, 'TRANS': 190} Chain: "B" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1727 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 209} 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: "C" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1629 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "D" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1744 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain: "E" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2078 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 13, 'TRANS': 246} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1609 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "G" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1812 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "H" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1483 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain: "I" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1493 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "J" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1471 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "K" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 809 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "L" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 885 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "N" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1187 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "O" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 942 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "P" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 943 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "Q" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1105 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "R" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain breaks: 1 Chain: "S" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1193 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "T" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1110 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "U" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 845 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "V" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 687 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "W" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "X" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1119 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "Y" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1061 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Z" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 558 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "a" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 770 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "b" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 609 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "c" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 487 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "f" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 546 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 65} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2466 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain breaks: 2 Chain: "d" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "e" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 233 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "1" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1584 Classifications: {'RNA': 74} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 30, 'rna3p_pyr': 28} Link IDs: {'rna2p': 15, 'rna3p': 58} Chain: "3" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'RNA': 22} Modifications used: {'rna2p_pyr': 9, 'rna3p_pur': 3, 'rna3p_pyr': 10} Link IDs: {'rna2p': 9, 'rna3p': 12} Chain: "i" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 884 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain: "j" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2025 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 6, 'TRANS': 245} Chain breaks: 2 Chain: "m" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 716 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 87} 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: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "k" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 1798 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 308} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 346} Chain breaks: 6 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1064 Unresolved non-hydrogen angles: 1351 Unresolved non-hydrogen dihedrals: 865 Unresolved non-hydrogen chiralities: 121 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 12, 'TYR:plan': 6, 'ASN:plan1': 15, 'TRP:plan': 2, 'HIS:plan': 9, 'PHE:plan': 10, 'GLU:plan': 19, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 488 Chain: "l" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 84 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "2" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Unusual residues: {' MG': 80} Classifications: {'undetermined': 80} Link IDs: {None: 79} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 70312 SG CYS a 23 105.295 95.007 147.129 1.00127.07 S ATOM 70333 SG CYS a 26 107.018 95.191 143.903 1.00102.94 S ATOM 70715 SG CYS a 74 104.552 97.839 144.512 1.00 83.30 S ATOM 72360 SG CYS f 124 74.383 75.521 32.592 1.00260.25 S Time building chain proxies: 32.51, per 1000 atoms: 0.39 Number of scatterers: 83760 At special positions: 0 Unit cell: (211.72, 263.98, 217.08, 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 3 29.99 S 97 16.00 P 1876 15.00 Mg 81 11.99 O 21070 8.00 N 15207 7.00 C 45426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.52 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 500 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 23 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 74 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 26 " pdb=" ZN f 501 " pdb="ZN ZN f 501 " - pdb=" SG CYS f 124 " 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10578 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 64 sheets defined 31.8% alpha, 16.7% beta 427 base pairs and 939 stacking pairs defined. Time for finding SS restraints: 24.79 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 49 through 65 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 169 through 184 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.698A pdb=" N PHE A 203 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.630A pdb=" N HIS B 79 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 80 " --> pdb=" O GLU B 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 80' Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 181 through 189 Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 225 through 231 removed outlier: 3.607A pdb=" N LEU B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 53 Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.926A pdb=" N ILE C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 Processing helix chain 'C' and resid 125 through 141 Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 211 through 228 removed outlier: 4.076A pdb=" N TYR C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 248 through 253 Processing helix chain 'D' and resid 6 through 29 Processing helix chain 'D' and resid 54 through 60 Processing helix chain 'D' and resid 63 through 77 removed outlier: 3.872A pdb=" N ASN D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 112 removed outlier: 3.579A pdb=" N GLY D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 130 Processing helix chain 'D' and resid 191 through 196 removed outlier: 3.737A pdb=" N THR D 196 " --> pdb=" O PRO D 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 51 removed outlier: 3.515A pdb=" N ASN E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 67 Processing helix chain 'E' and resid 247 through 258 Processing helix chain 'F' and resid 32 through 37 Processing helix chain 'F' and resid 84 through 89 Processing helix chain 'F' and resid 90 through 100 Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.603A pdb=" N ALA F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 143 removed outlier: 3.523A pdb=" N VAL F 134 " --> pdb=" O ASN F 130 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY F 143 " --> pdb=" O ILE F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 186 Processing helix chain 'F' and resid 191 through 205 Processing helix chain 'F' and resid 210 through 225 Processing helix chain 'G' and resid 20 through 25 removed outlier: 3.802A pdb=" N VAL G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 180 through 224 removed outlier: 3.657A pdb=" N ALA G 198 " --> pdb=" O LYS G 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU G 218 " --> pdb=" O LYS G 214 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU G 222 " --> pdb=" O GLU G 218 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA G 224 " --> pdb=" O LYS G 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 29 Processing helix chain 'H' and resid 67 through 73 Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'H' and resid 113 through 117 removed outlier: 3.920A pdb=" N THR H 117 " --> pdb=" O ARG H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 165 through 177 Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 88 through 93 removed outlier: 4.248A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR I 93 " --> pdb=" O GLU I 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 88 through 93' Processing helix chain 'I' and resid 106 through 114 Processing helix chain 'I' and resid 137 through 148 removed outlier: 3.821A pdb=" N GLU I 141 " --> pdb=" O SER I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 164 Processing helix chain 'I' and resid 186 through 201 removed outlier: 3.720A pdb=" N ALA I 191 " --> pdb=" O GLY I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 35 Processing helix chain 'J' and resid 38 through 62 removed outlier: 4.047A pdb=" N ILE J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 84 removed outlier: 3.988A pdb=" N ASN J 74 " --> pdb=" O LEU J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 99 Processing helix chain 'J' and resid 108 through 117 removed outlier: 4.262A pdb=" N TYR J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU J 116 " --> pdb=" O GLN J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 131 Processing helix chain 'J' and resid 170 through 182 Processing helix chain 'K' and resid 4 through 19 Processing helix chain 'K' and resid 38 through 51 removed outlier: 3.617A pdb=" N VAL K 42 " --> pdb=" O LYS K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 80 Processing helix chain 'L' and resid 46 through 51 Processing helix chain 'M' and resid 21 through 32 Processing helix chain 'M' and resid 38 through 47 removed outlier: 4.194A pdb=" N ARG M 47 " --> pdb=" O LYS M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 74 Processing helix chain 'M' and resid 84 through 93 removed outlier: 3.507A pdb=" N LEU M 88 " --> pdb=" O ASP M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 132 removed outlier: 4.119A pdb=" N LEU M 128 " --> pdb=" O ARG M 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 Processing helix chain 'N' and resid 46 through 58 Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 78 Processing helix chain 'N' and resid 86 through 105 Processing helix chain 'N' and resid 108 through 132 Processing helix chain 'N' and resid 145 through 150 Processing helix chain 'O' and resid 56 through 73 removed outlier: 3.550A pdb=" N ALA O 60 " --> pdb=" O SER O 56 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU O 73 " --> pdb=" O ALA O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 109 removed outlier: 3.849A pdb=" N GLY O 109 " --> pdb=" O LEU O 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 26 removed outlier: 3.990A pdb=" N LEU P 25 " --> pdb=" O ASP P 21 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU P 26 " --> pdb=" O LEU P 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 21 through 26' Processing helix chain 'P' and resid 29 through 36 removed outlier: 3.737A pdb=" N PHE P 33 " --> pdb=" O PRO P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 47 Processing helix chain 'P' and resid 55 through 67 Processing helix chain 'P' and resid 115 through 119 Processing helix chain 'Q' and resid 44 through 56 removed outlier: 3.813A pdb=" N VAL Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Proline residue: Q 51 - end of helix Processing helix chain 'Q' and resid 57 through 61 Processing helix chain 'Q' and resid 74 through 97 Processing helix chain 'Q' and resid 98 through 110 Processing helix chain 'R' and resid 6 through 20 removed outlier: 3.521A pdb=" N LYS R 10 " --> pdb=" O THR R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 39 Processing helix chain 'R' and resid 43 through 62 Processing helix chain 'R' and resid 71 through 81 removed outlier: 3.785A pdb=" N GLU R 76 " --> pdb=" O LYS R 72 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU R 77 " --> pdb=" O LEU R 73 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU R 79 " --> pdb=" O GLU R 75 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS R 81 " --> pdb=" O GLU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 114 Processing helix chain 'S' and resid 28 through 33 Processing helix chain 'S' and resid 39 through 51 Processing helix chain 'S' and resid 62 through 75 Processing helix chain 'S' and resid 76 through 80 removed outlier: 3.823A pdb=" N LYS S 80 " --> pdb=" O THR S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 119 Processing helix chain 'S' and resid 121 through 130 Processing helix chain 'T' and resid 10 through 25 Processing helix chain 'T' and resid 53 through 68 Processing helix chain 'T' and resid 72 through 80 Processing helix chain 'T' and resid 97 through 112 removed outlier: 3.781A pdb=" N ASN T 101 " --> pdb=" O SER T 97 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG T 102 " --> pdb=" O GLY T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 144 Processing helix chain 'U' and resid 30 through 49 removed outlier: 3.536A pdb=" N LEU U 34 " --> pdb=" O LYS U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 104 Processing helix chain 'V' and resid 56 through 63 Processing helix chain 'V' and resid 64 through 76 removed outlier: 4.075A pdb=" N GLN V 74 " --> pdb=" O ASN V 70 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN V 75 " --> pdb=" O ARG V 71 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP V 76 " --> pdb=" O LEU V 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 21 Processing helix chain 'W' and resid 32 through 45 Processing helix chain 'W' and resid 85 through 94 Processing helix chain 'W' and resid 112 through 120 Processing helix chain 'X' and resid 12 through 24 Processing helix chain 'X' and resid 26 through 35 removed outlier: 3.785A pdb=" N GLY X 35 " --> pdb=" O LYS X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 92 through 97 removed outlier: 3.680A pdb=" N ASP X 97 " --> pdb=" O LEU X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 137 Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 95 Processing helix chain 'Y' and resid 104 through 118 Processing helix chain 'Y' and resid 122 through 135 Processing helix chain 'Z' and resid 43 through 54 Processing helix chain 'Z' and resid 61 through 68 Processing helix chain 'Z' and resid 73 through 84 removed outlier: 4.056A pdb=" N ARG Z 77 " --> pdb=" O GLY Z 73 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL Z 78 " --> pdb=" O SER Z 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 50 through 56 Processing helix chain 'a' and resid 74 through 79 removed outlier: 3.723A pdb=" N ILE a 79 " --> pdb=" O SER a 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 18 removed outlier: 3.754A pdb=" N ALA b 16 " --> pdb=" O ALA b 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 289 through 293 removed outlier: 3.780A pdb=" N ASP g 293 " --> pdb=" O LYS g 290 " (cutoff:3.500A) Processing helix chain 'd' and resid 32 through 36 removed outlier: 3.582A pdb=" N LEU d 36 " --> pdb=" O LYS d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 45 Processing helix chain 'd' and resid 46 through 51 Processing helix chain 'e' and resid 31 through 45 removed outlier: 3.756A pdb=" N VAL e 45 " --> pdb=" O THR e 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 25 removed outlier: 3.783A pdb=" N ARG h 6 " --> pdb=" O ARG h 2 " (cutoff:3.500A) Processing helix chain 'i' and resid 63 through 67 removed outlier: 4.323A pdb=" N LYS i 67 " --> pdb=" O LYS i 64 " (cutoff:3.500A) Processing helix chain 'i' and resid 96 through 107 Processing helix chain 'j' and resid 94 through 119 removed outlier: 3.668A pdb=" N ARG j 113 " --> pdb=" O HIS j 109 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR j 114 " --> pdb=" O SER j 110 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS j 115 " --> pdb=" O ILE j 111 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA j 116 " --> pdb=" O LEU j 112 " (cutoff:3.500A) Processing helix chain 'j' and resid 122 through 131 Processing helix chain 'j' and resid 131 through 138 Processing helix chain 'j' and resid 140 through 151 Processing helix chain 'j' and resid 153 through 158 removed outlier: 3.611A pdb=" N GLY j 157 " --> pdb=" O THR j 153 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE j 158 " --> pdb=" O VAL j 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 153 through 158' Processing helix chain 'j' and resid 162 through 174 removed outlier: 3.818A pdb=" N LEU j 166 " --> pdb=" O SER j 162 " (cutoff:3.500A) Processing helix chain 'j' and resid 196 through 210 removed outlier: 3.967A pdb=" N ASP j 210 " --> pdb=" O LYS j 206 " (cutoff:3.500A) Processing helix chain 'j' and resid 238 through 254 removed outlier: 4.120A pdb=" N GLU j 242 " --> pdb=" O GLN j 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN j 243 " --> pdb=" O LYS j 239 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 62 Processing helix chain 'm' and resid 85 through 95 Processing helix chain 'k' and resid 113 through 121 Processing helix chain 'k' and resid 200 through 209 removed outlier: 3.573A pdb=" N SER k 206 " --> pdb=" O SER k 202 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA k 209 " --> pdb=" O LEU k 205 " (cutoff:3.500A) Processing helix chain 'k' and resid 226 through 240 Processing helix chain 'k' and resid 250 through 254 removed outlier: 3.670A pdb=" N MET k 254 " --> pdb=" O VAL k 251 " (cutoff:3.500A) Processing helix chain 'k' and resid 257 through 270 Processing helix chain 'k' and resid 290 through 301 removed outlier: 3.517A pdb=" N VAL k 294 " --> pdb=" O ASN k 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 140 Processing sheet with id= A, first strand: chain 'A' and resid 24 through 25 removed outlier: 7.288A pdb=" N VAL A 47 " --> pdb=" O TYR A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.949A pdb=" N ALA A 75 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 74 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 121 " --> pdb=" O ILE A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 42 through 47 removed outlier: 6.774A pdb=" N ILE B 32 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS B 45 " --> pdb=" O TYR B 30 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR B 30 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LEU B 96 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP B 31 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR B 98 " --> pdb=" O ASP B 31 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LYS B 33 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N PHE B 100 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASN B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL B 91 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU B 97 " --> pdb=" O ASP B 89 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 120 through 128 removed outlier: 7.020A pdb=" N PHE B 142 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN B 209 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 120 through 128 removed outlier: 6.591A pdb=" N VAL B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 84 through 91 removed outlier: 5.044A pdb=" N VAL C 85 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL C 108 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN C 87 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 146 through 147 Processing sheet with id= H, first strand: chain 'C' and resid 163 through 166 removed outlier: 3.724A pdb=" N GLY C 165 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 172 " --> pdb=" O GLY C 165 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C 204 " --> pdb=" O ARG C 173 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 34 through 41 removed outlier: 3.770A pdb=" N GLY D 36 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR D 46 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N TYR D 87 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE D 48 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLU D 89 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE D 50 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 148 through 154 Processing sheet with id= K, first strand: chain 'E' and resid 42 through 43 Processing sheet with id= L, first strand: chain 'E' and resid 70 through 71 removed outlier: 3.700A pdb=" N ASN E 98 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.879A pdb=" N VAL E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.108A pdb=" N LYS E 128 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASP E 171 " --> pdb=" O LYS E 161 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 192 through 193 Processing sheet with id= P, first strand: chain 'E' and resid 207 through 211 Processing sheet with id= Q, first strand: chain 'F' and resid 146 through 149 removed outlier: 3.827A pdb=" N THR F 149 " --> pdb=" O GLN F 160 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN F 160 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ALA F 161 " --> pdb=" O ASN c 43 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS c 45 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP F 163 " --> pdb=" O LYS c 45 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN c 27 " --> pdb=" O VAL c 15 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL c 15 " --> pdb=" O GLN c 27 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ARG c 29 " --> pdb=" O ILE c 13 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR c 8 " --> pdb=" O LEU c 56 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 13 through 17 removed outlier: 3.583A pdb=" N LEU G 109 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE G 113 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY G 54 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE G 112 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE G 52 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N THR G 114 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE G 50 " --> pdb=" O THR G 114 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 72 through 78 Processing sheet with id= T, first strand: chain 'G' and resid 160 through 163 removed outlier: 3.852A pdb=" N TYR G 169 " --> pdb=" O VAL G 162 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 46 through 50 Processing sheet with id= V, first strand: chain 'H' and resid 180 through 184 removed outlier: 3.759A pdb=" N GLN H 180 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE W 50 " --> pdb=" O TYR H 142 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 3 through 4 Processing sheet with id= X, first strand: chain 'I' and resid 42 through 48 removed outlier: 6.526A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR I 48 " --> pdb=" O ASN I 52 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR I 36 " --> pdb=" O LEU I 96 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 167 through 169 removed outlier: 6.382A pdb=" N GLN I 103 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL I 81 " --> pdb=" O GLN I 103 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG I 74 " --> pdb=" O PHE I 65 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE I 65 " --> pdb=" O ARG I 74 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY I 182 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 70 through 77 removed outlier: 6.510A pdb=" N VAL L 85 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N PHE L 137 " --> pdb=" O ASN L 106 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N VAL L 139 " --> pdb=" O PRO L 108 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS L 110 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N LYS L 141 " --> pdb=" O HIS L 110 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR L 124 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N VAL L 142 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE L 122 " --> pdb=" O VAL L 142 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 79 through 80 removed outlier: 6.225A pdb=" N ALA M 53 " --> pdb=" O ILE M 80 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'O' and resid 14 through 16 removed outlier: 6.075A pdb=" N GLY O 15 " --> pdb=" O HIS O 80 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LYS O 82 " --> pdb=" O GLY O 15 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL O 79 " --> pdb=" O GLY O 113 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE O 115 " --> pdb=" O VAL O 79 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE O 81 " --> pdb=" O ILE O 115 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP O 117 " --> pdb=" O ILE O 81 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE O 83 " --> pdb=" O ASP O 117 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'O' and resid 30 through 31 removed outlier: 7.118A pdb=" N VAL O 30 " --> pdb=" O ILE O 39 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'P' and resid 76 through 78 Processing sheet with id= AE, first strand: chain 'Q' and resid 7 through 13 removed outlier: 5.855A pdb=" N LEU Q 28 " --> pdb=" O ILE Q 65 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL Q 67 " --> pdb=" O LEU Q 28 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LYS Q 30 " --> pdb=" O VAL Q 67 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL Q 69 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'R' and resid 101 through 102 removed outlier: 4.003A pdb=" N VAL R 102 " --> pdb=" O SER R 120 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'S' and resid 15 through 16 Processing sheet with id= AH, first strand: chain 'T' and resid 82 through 83 Processing sheet with id= AI, first strand: chain 'T' and resid 114 through 116 Processing sheet with id= AJ, first strand: chain 'U' and resid 51 through 56 removed outlier: 5.375A pdb=" N LYS U 52 " --> pdb=" O GLU U 94 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU U 94 " --> pdb=" O LYS U 52 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLY U 54 " --> pdb=" O ASP U 92 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASP U 92 " --> pdb=" O GLY U 54 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'U' and resid 61 through 68 Processing sheet with id= AL, first strand: chain 'V' and resid 32 through 41 removed outlier: 3.836A pdb=" N GLN V 38 " --> pdb=" O GLU V 49 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLU V 49 " --> pdb=" O GLN V 38 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N ASP V 40 " --> pdb=" O PRO V 47 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'W' and resid 72 through 73 removed outlier: 3.613A pdb=" N PHE W 128 " --> pdb=" O GLY W 73 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE W 128 " --> pdb=" O TYR W 101 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'X' and resid 50 through 53 removed outlier: 10.347A pdb=" N PHE X 122 " --> pdb=" O LYS X 82 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N THR X 84 " --> pdb=" O PHE X 122 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL X 124 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE X 86 " --> pdb=" O VAL X 124 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N LYS X 126 " --> pdb=" O PHE X 86 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU X 103 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL X 127 " --> pdb=" O GLU X 101 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU X 101 " --> pdb=" O VAL X 127 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Y' and resid 6 through 13 removed outlier: 5.790A pdb=" N ILE Y 7 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 7 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR Y 9 " --> pdb=" O ASP Y 26 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP Y 26 " --> pdb=" O THR Y 9 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LYS Y 11 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL Y 24 " --> pdb=" O LYS Y 11 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL Y 25 " --> pdb=" O GLY Y 71 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY Y 67 " --> pdb=" O HIS Y 29 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Z' and resid 59 through 60 removed outlier: 3.744A pdb=" N TYR Z 101 " --> pdb=" O VAL Z 60 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= AR, first strand: chain 'a' and resid 40 through 43 Processing sheet with id= AS, first strand: chain 'b' and resid 44 through 46 removed outlier: 3.517A pdb=" N THR b 44 " --> pdb=" O VAL b 35 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP b 34 " --> pdb=" O ARG b 80 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG b 80 " --> pdb=" O ASP b 34 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER b 78 " --> pdb=" O LYS b 36 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'b' and resid 64 through 66 Processing sheet with id= AU, first strand: chain 'f' and resid 131 through 132 Processing sheet with id= AV, first strand: chain 'g' and resid 6 through 14 removed outlier: 4.697A pdb=" N LEU g 8 " --> pdb=" O MET g 323 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N MET g 323 " --> pdb=" O LEU g 8 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU g 10 " --> pdb=" O GLN g 321 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLN g 321 " --> pdb=" O LEU g 10 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY g 12 " --> pdb=" O VAL g 319 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL g 319 " --> pdb=" O GLY g 12 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE g 309 " --> pdb=" O LEU g 299 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU g 299 " --> pdb=" O PHE g 309 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY g 311 " --> pdb=" O VAL g 297 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'g' and resid 23 through 24 removed outlier: 6.201A pdb=" N LEU g 43 " --> pdb=" O SER g 61 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER g 61 " --> pdb=" O LEU g 43 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER g 45 " --> pdb=" O VAL g 59 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'g' and resid 69 through 74 removed outlier: 3.750A pdb=" N ASP g 71 " --> pdb=" O ALA g 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG g 91 " --> pdb=" O SER g 83 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER g 85 " --> pdb=" O THR g 89 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR g 89 " --> pdb=" O SER g 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA g 102 " --> pdb=" O LEU g 92 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN g 94 " --> pdb=" O SER g 100 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER g 100 " --> pdb=" O ASN g 94 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'g' and resid 111 through 116 removed outlier: 6.889A pdb=" N ALA g 126 " --> pdb=" O LEU g 112 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL g 114 " --> pdb=" O ILE g 124 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE g 124 " --> pdb=" O VAL g 114 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR g 143 " --> pdb=" O VAL g 134 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'g' and resid 154 through 158 removed outlier: 4.519A pdb=" N THR g 173 " --> pdb=" O ALA g 158 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA g 197 " --> pdb=" O SER g 185 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'g' and resid 208 through 211 removed outlier: 7.132A pdb=" N ILE g 227 " --> pdb=" O ASN g 240 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN g 240 " --> pdb=" O ILE g 227 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL g 229 " --> pdb=" O PHE g 238 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'g' and resid 249 through 252 removed outlier: 3.812A pdb=" N ALA g 249 " --> pdb=" O ALA g 262 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP g 271 " --> pdb=" O LEU g 277 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU g 277 " --> pdb=" O ASP g 271 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'd' and resid 30 through 31 removed outlier: 3.817A pdb=" N ILE d 38 " --> pdb=" O ILE d 31 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'i' and resid 33 through 40 removed outlier: 4.883A pdb=" N ILE i 38 " --> pdb=" O SER i 50 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N SER i 50 " --> pdb=" O ILE i 38 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N MET i 58 " --> pdb=" O CYS i 89 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL i 91 " --> pdb=" O MET i 58 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N HIS i 60 " --> pdb=" O VAL i 91 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N HIS i 93 " --> pdb=" O HIS i 60 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL i 91 " --> pdb=" O SER i 80 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER i 80 " --> pdb=" O VAL i 91 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'j' and resid 19 through 23 removed outlier: 3.528A pdb=" N GLY j 44 " --> pdb=" O VAL j 34 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLU j 43 " --> pdb=" O ILE j 83 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N LEU j 85 " --> pdb=" O GLU j 43 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET j 45 " --> pdb=" O LEU j 85 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP j 84 " --> pdb=" O LEU j 74 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'j' and resid 219 through 222 Processing sheet with id= BG, first strand: chain 'm' and resid 66 through 70 removed outlier: 3.670A pdb=" N THR m 41 " --> pdb=" O ARG m 29 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'k' and resid 141 through 149 removed outlier: 4.502A pdb=" N ALA k 143 " --> pdb=" O PHE k 191 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS k 149 " --> pdb=" O LEU k 185 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU k 185 " --> pdb=" O LYS k 149 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR k 105 " --> pdb=" O VAL k 192 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA k 214 " --> pdb=" O ILE k 245 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU k 247 " --> pdb=" O ALA k 214 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU k 216 " --> pdb=" O LEU k 247 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'k' and resid 340 through 344 removed outlier: 5.266A pdb=" N ILE k 342 " --> pdb=" O ILE k 316 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE k 316 " --> pdb=" O ILE k 342 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN k 344 " --> pdb=" O ARG k 314 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS k 371 " --> pdb=" O PRO k 357 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'k' and resid 347 through 348 Processing sheet with id= BK, first strand: chain 'k' and resid 381 through 382 Processing sheet with id= BL, first strand: chain 'k' and resid 425 through 436 removed outlier: 9.770A pdb=" N ILE k 426 " --> pdb=" O SER k 489 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N SER k 489 " --> pdb=" O ILE k 426 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR k 428 " --> pdb=" O LEU k 487 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N GLY k 472 " --> pdb=" O THR k 488 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N VAL k 461 " --> pdb=" O ARG k 504 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ARG k 504 " --> pdb=" O VAL k 461 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE k 499 " --> pdb=" O ALA k 515 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA k 515 " --> pdb=" O ILE k 499 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG k 503 " --> pdb=" O LEU k 511 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU k 511 " --> pdb=" O ARG k 503 " (cutoff:3.500A) 1616 hydrogen bonds defined for protein. 4623 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1051 hydrogen bonds 1796 hydrogen bond angles 0 basepair planarities 427 basepair parallelities 939 stacking parallelities Total time for adding SS restraints: 59.91 Time building geometry restraints manager: 34.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11273 1.33 - 1.45: 33467 1.45 - 1.57: 40422 1.57 - 1.70: 3752 1.70 - 1.82: 152 Bond restraints: 89066 Sorted by residual: bond pdb=" CA ASN k 496 " pdb=" C ASN k 496 " ideal model delta sigma weight residual 1.525 1.647 -0.122 1.25e-02 6.40e+03 9.46e+01 bond pdb=" N GLU k 497 " pdb=" CA GLU k 497 " ideal model delta sigma weight residual 1.457 1.567 -0.110 1.29e-02 6.01e+03 7.28e+01 bond pdb=" CA GLU k 497 " pdb=" C GLU k 497 " ideal model delta sigma weight residual 1.523 1.631 -0.108 1.34e-02 5.57e+03 6.48e+01 bond pdb=" CA ALA U 97 " pdb=" C ALA U 97 " ideal model delta sigma weight residual 1.519 1.542 -0.024 5.30e-03 3.56e+04 2.02e+01 bond pdb=" CA PRO a 97 " pdb=" C PRO a 97 " ideal model delta sigma weight residual 1.517 1.555 -0.038 9.30e-03 1.16e+04 1.68e+01 ... (remaining 89061 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.33: 11153 106.33 - 113.31: 48239 113.31 - 120.30: 34809 120.30 - 127.28: 30926 127.28 - 134.27: 4230 Bond angle restraints: 129357 Sorted by residual: angle pdb=" N GLU k 497 " pdb=" CA GLU k 497 " pdb=" C GLU k 497 " ideal model delta sigma weight residual 110.80 133.61 -22.81 2.13e+00 2.20e-01 1.15e+02 angle pdb=" N VAL k 210 " pdb=" CA VAL k 210 " pdb=" C VAL k 210 " ideal model delta sigma weight residual 113.71 105.62 8.09 9.50e-01 1.11e+00 7.25e+01 angle pdb=" N TYR k 434 " pdb=" CA TYR k 434 " pdb=" C TYR k 434 " ideal model delta sigma weight residual 108.79 121.18 -12.39 1.53e+00 4.27e-01 6.55e+01 angle pdb=" O3' C 2 114 " pdb=" C3' C 2 114 " pdb=" C2' C 2 114 " ideal model delta sigma weight residual 109.50 121.37 -11.87 1.50e+00 4.44e-01 6.26e+01 angle pdb=" O3' G 2 538 " pdb=" C3' G 2 538 " pdb=" C2' G 2 538 " ideal model delta sigma weight residual 109.50 121.30 -11.80 1.50e+00 4.44e-01 6.19e+01 ... (remaining 129352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 48128 35.95 - 71.91: 5296 71.91 - 107.86: 690 107.86 - 143.81: 40 143.81 - 179.77: 79 Dihedral angle restraints: 54233 sinusoidal: 37858 harmonic: 16375 Sorted by residual: dihedral pdb=" C5' U 3 19 " pdb=" C4' U 3 19 " pdb=" C3' U 3 19 " pdb=" O3' U 3 19 " ideal model delta sinusoidal sigma weight residual 147.00 72.48 74.52 1 8.00e+00 1.56e-02 1.10e+02 dihedral pdb=" C5' A 2 810 " pdb=" C4' A 2 810 " pdb=" C3' A 2 810 " pdb=" O3' A 2 810 " ideal model delta sinusoidal sigma weight residual 147.00 76.15 70.85 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C5' C 2 130 " pdb=" C4' C 2 130 " pdb=" C3' C 2 130 " pdb=" O3' C 2 130 " ideal model delta sinusoidal sigma weight residual 147.00 77.18 69.82 1 8.00e+00 1.56e-02 9.83e+01 ... (remaining 54230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 13327 0.147 - 0.294: 2706 0.294 - 0.441: 96 0.441 - 0.589: 28 0.589 - 0.736: 10 Chirality restraints: 16167 Sorted by residual: chirality pdb=" CA TYR S 42 " pdb=" N TYR S 42 " pdb=" C TYR S 42 " pdb=" CB TYR S 42 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" C3' C 2 139 " pdb=" C4' C 2 139 " pdb=" O3' C 2 139 " pdb=" C2' C 2 139 " 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' G 2 538 " pdb=" C4' G 2 538 " pdb=" O3' G 2 538 " pdb=" C2' G 2 538 " both_signs ideal model delta sigma weight residual False -2.74 -2.10 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 16164 not shown) Planarity restraints: 9565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE k 495 " -0.058 2.00e-02 2.50e+03 1.16e-01 1.34e+02 pdb=" C ILE k 495 " 0.200 2.00e-02 2.50e+03 pdb=" O ILE k 495 " -0.079 2.00e-02 2.50e+03 pdb=" N ASN k 496 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN X 63 " 0.083 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO X 64 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO X 64 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO X 64 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA N 22 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO N 23 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO N 23 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO N 23 " 0.055 5.00e-02 4.00e+02 ... (remaining 9562 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 11 1.84 - 2.61: 1043 2.61 - 3.37: 98175 3.37 - 4.14: 251884 4.14 - 4.90: 368749 Nonbonded interactions: 719862 Sorted by model distance: nonbonded pdb=" CG GLU j 196 " pdb=" CB VAL k 378 " model vdw 1.076 3.870 nonbonded pdb=" O3' A 1 76 " pdb=" C MET k 601 " model vdw 1.176 3.270 nonbonded pdb=" N3 A 1 76 " pdb=" O GLU k 383 " model vdw 1.330 3.120 nonbonded pdb=" N6 A 1 76 " pdb=" O GLN k 384 " model vdw 1.330 2.520 nonbonded pdb=" C6 A 1 76 " pdb=" O GLN k 384 " model vdw 1.521 3.260 ... (remaining 719857 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.050 Extract box with map and model: 9.040 Check model and map are aligned: 0.900 Set scattering table: 0.560 Process input model: 223.170 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.210 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:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 239.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 : 0.007 0.122 89066 Z= 0.441 Angle : 1.297 22.812 129357 Z= 0.861 Chirality : 0.104 0.736 16167 Planarity : 0.005 0.125 9565 Dihedral : 25.180 179.767 43655 Min Nonbonded Distance : 1.076 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 4.95 % Allowed : 11.56 % Favored : 83.50 % Rotamer: Outliers : 12.47 % Allowed : 15.76 % Favored : 71.77 % Cbeta Deviations : 1.21 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 1.38 % Twisted General : 0.02 % 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: -2.31 (0.10), residues: 5581 helix: 1.08 (0.11), residues: 1668 sheet: -1.89 (0.15), residues: 949 loop : -3.13 (0.10), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP g 20 HIS 0.010 0.001 HIS T 91 PHE 0.023 0.002 PHE W 37 TYR 0.037 0.002 TYR S 42 ARG 0.024 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2170 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 562 poor density : 1608 time to evaluate : 4.771 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 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 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: 562 outliers final: 95 residues processed: 1942 average time/residue: 0.8734 time to fit residues: 2804.6119 Evaluate side-chains 1085 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 990 time to evaluate : 4.747 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 2 residues processed: 95 average time/residue: 0.7857 time to fit residues: 134.4197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 623 optimal weight: 20.0000 chunk 559 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 191 optimal weight: 0.9990 chunk 377 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 chunk 578 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 351 optimal weight: 9.9990 chunk 430 optimal weight: 2.9990 chunk 670 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 ASN A 83 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN B 42 ASN B 99 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN C 64 HIS ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 233 ASN C 238 GLN D 56 GLN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN D 165 ASN E 36 HIS E 67 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS E 209 HIS E 224 ASN E 259 HIS F 37 GLN F 39 GLN F 81 ASN F 88 GLN F 102 ASN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 ASN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN I 9 HIS ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 HIS ** I 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 HIS ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 ASN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 GLN O 29 HIS O 99 GLN P 82 ASN ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 GLN R 105 GLN R 111 ASN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 78 HIS S 87 ASN S 136 GLN T 43 ASN T 127 ASN ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 HIS W 80 ASN ** W 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 113 HIS ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 34 ASN ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 85 ASN ** Z 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 11 ASN b 9 HIS ** c 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 ASN f 133 HIS ** g 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 240 ASN g 292 GLN g 326 ASN d 5 ASN d 27 HIS e 17 GLN i 44 ASN i 106 GLN j 5 HIS j 25 GLN j 26 GLN j 103 GLN j 109 HIS m 43 GLN ** m 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 102 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 89066 Z= 0.300 Angle : 0.853 14.855 129357 Z= 0.439 Chirality : 0.046 0.411 16167 Planarity : 0.006 0.144 9565 Dihedral : 25.033 179.923 33102 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 2.35 % Allowed : 10.11 % Favored : 87.55 % Rotamer: Outliers : 6.24 % Allowed : 24.19 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 2.29 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.11), residues: 5581 helix: 1.69 (0.13), residues: 1704 sheet: -1.53 (0.16), residues: 919 loop : -2.86 (0.10), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP V 83 HIS 0.015 0.002 HIS E 197 PHE 0.038 0.003 PHE C 220 TYR 0.043 0.003 TYR S 42 ARG 0.016 0.001 ARG a 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1350 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1069 time to evaluate : 4.809 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 281 outliers final: 135 residues processed: 1261 average time/residue: 0.8469 time to fit residues: 1820.6182 Evaluate side-chains 1013 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 878 time to evaluate : 4.697 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 135 outliers final: 1 residues processed: 135 average time/residue: 0.6759 time to fit residues: 176.9246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 372 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 557 optimal weight: 8.9990 chunk 456 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 671 optimal weight: 10.0000 chunk 725 optimal weight: 7.9990 chunk 597 optimal weight: 20.0000 chunk 665 optimal weight: 20.0000 chunk 228 optimal weight: 7.9990 chunk 538 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 220 GLN B 232 HIS ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN C 233 ASN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN G 65 GLN G 201 GLN H 22 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN I 111 GLN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 GLN ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 137 HIS U 98 HIS ** V 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 33 GLN V 35 ASN W 70 ASN W 92 ASN X 89 ASN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 38 HIS ** c 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 70 GLN g 321 GLN d 10 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 89066 Z= 0.287 Angle : 0.784 13.977 129357 Z= 0.401 Chirality : 0.044 0.419 16167 Planarity : 0.006 0.147 9565 Dihedral : 25.002 179.828 33102 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 2.08 % Allowed : 11.06 % Favored : 86.87 % Rotamer: Outliers : 4.42 % Allowed : 26.03 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.11), residues: 5581 helix: 1.26 (0.13), residues: 1702 sheet: -1.43 (0.16), residues: 921 loop : -2.73 (0.10), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 53 HIS 0.022 0.002 HIS P 128 PHE 0.039 0.002 PHE J 71 TYR 0.035 0.002 TYR W 101 ARG 0.009 0.001 ARG i 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 986 time to evaluate : 4.827 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 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: 199 outliers final: 89 residues processed: 1120 average time/residue: 0.8200 time to fit residues: 1577.0955 Evaluate side-chains 931 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 842 time to evaluate : 4.777 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 89 outliers final: 1 residues processed: 89 average time/residue: 0.6443 time to fit residues: 113.9480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 663 optimal weight: 1.9990 chunk 504 optimal weight: 9.9990 chunk 348 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 320 optimal weight: 0.9980 chunk 450 optimal weight: 0.5980 chunk 673 optimal weight: 20.0000 chunk 713 optimal weight: 8.9990 chunk 352 optimal weight: 8.9990 chunk 638 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN D 67 ASN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN F 37 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 HIS ** T 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 33 GLN ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 GLN ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS ** c 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 ASN g 53 GLN j 140 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 89066 Z= 0.232 Angle : 0.741 13.566 129357 Z= 0.374 Chirality : 0.042 0.441 16167 Planarity : 0.005 0.149 9565 Dihedral : 24.900 179.640 33102 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 1.95 % Allowed : 10.36 % Favored : 87.69 % Rotamer: Outliers : 3.77 % Allowed : 27.72 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.02 % 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: -1.77 (0.11), residues: 5581 helix: 1.13 (0.13), residues: 1713 sheet: -1.40 (0.17), residues: 907 loop : -2.65 (0.10), residues: 2961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 235 HIS 0.017 0.002 HIS P 128 PHE 0.038 0.002 PHE J 71 TYR 0.036 0.002 TYR W 101 ARG 0.009 0.001 ARG G 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 981 time to evaluate : 4.722 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 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: 170 outliers final: 78 residues processed: 1088 average time/residue: 0.8194 time to fit residues: 1533.3410 Evaluate side-chains 907 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 829 time to evaluate : 4.753 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 78 outliers final: 1 residues processed: 78 average time/residue: 0.6398 time to fit residues: 100.3646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 594 optimal weight: 5.9990 chunk 404 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 531 optimal weight: 8.9990 chunk 294 optimal weight: 0.9990 chunk 608 optimal weight: 7.9990 chunk 493 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 364 optimal weight: 0.0980 chunk 640 optimal weight: 0.0270 chunk 180 optimal weight: 8.9990 overall best weight: 2.0244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 ASN D 179 GLN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 24 ASN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 80 ASN W 92 ASN ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 38 HIS ** c 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 89066 Z= 0.189 Angle : 0.712 14.612 129357 Z= 0.358 Chirality : 0.040 0.406 16167 Planarity : 0.005 0.153 9565 Dihedral : 24.738 179.927 33102 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 1.83 % Allowed : 10.48 % Favored : 87.69 % Rotamer: Outliers : 3.04 % Allowed : 29.76 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.06 % 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: -1.71 (0.11), residues: 5581 helix: 1.04 (0.13), residues: 1711 sheet: -1.21 (0.17), residues: 935 loop : -2.58 (0.11), residues: 2935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP M 91 HIS 0.010 0.001 HIS P 128 PHE 0.041 0.002 PHE J 71 TYR 0.030 0.002 TYR E 103 ARG 0.010 0.001 ARG e 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 971 time to evaluate : 5.081 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 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: 137 outliers final: 54 residues processed: 1060 average time/residue: 0.8177 time to fit residues: 1493.9340 Evaluate side-chains 888 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 834 time to evaluate : 5.398 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 2 residues processed: 54 average time/residue: 0.7506 time to fit residues: 79.2432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 240 optimal weight: 7.9990 chunk 642 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 418 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 714 optimal weight: 50.0000 chunk 592 optimal weight: 7.9990 chunk 330 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 374 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 87 GLN P 82 ASN P 104 GLN ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS S 19 ASN ** T 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 89066 Z= 0.285 Angle : 0.745 14.169 129357 Z= 0.377 Chirality : 0.041 0.376 16167 Planarity : 0.005 0.151 9565 Dihedral : 24.745 179.554 33102 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 1.74 % Allowed : 11.00 % Favored : 87.26 % Rotamer: Outliers : 2.86 % Allowed : 31.25 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.11), residues: 5581 helix: 0.93 (0.13), residues: 1700 sheet: -1.27 (0.16), residues: 969 loop : -2.58 (0.11), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP M 91 HIS 0.011 0.001 HIS P 128 PHE 0.053 0.002 PHE I 192 TYR 0.042 0.002 TYR J 43 ARG 0.008 0.001 ARG X 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 860 time to evaluate : 4.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 revert: symmetry clash outliers start: 129 outliers final: 72 residues processed: 940 average time/residue: 0.8394 time to fit residues: 1357.0029 Evaluate side-chains 864 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 792 time to evaluate : 4.895 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 72 outliers final: 1 residues processed: 72 average time/residue: 0.6972 time to fit residues: 98.0424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 688 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 chunk 406 optimal weight: 5.9990 chunk 521 optimal weight: 8.9990 chunk 404 optimal weight: 5.9990 chunk 601 optimal weight: 1.9990 chunk 398 optimal weight: 0.9980 chunk 711 optimal weight: 20.0000 chunk 445 optimal weight: 3.9990 chunk 433 optimal weight: 9.9990 chunk 328 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 29 HIS ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 ASN ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 89066 Z= 0.233 Angle : 0.718 13.509 129357 Z= 0.362 Chirality : 0.040 0.370 16167 Planarity : 0.005 0.154 9565 Dihedral : 24.700 179.319 33102 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 1.63 % Allowed : 10.75 % Favored : 87.62 % Rotamer: Outliers : 1.89 % Allowed : 32.58 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.11), residues: 5581 helix: 0.87 (0.13), residues: 1703 sheet: -1.31 (0.16), residues: 972 loop : -2.56 (0.11), residues: 2906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP S 84 HIS 0.009 0.001 HIS P 128 PHE 0.069 0.002 PHE I 192 TYR 0.040 0.002 TYR I 193 ARG 0.010 0.001 ARG I 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 876 time to evaluate : 4.846 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 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: 85 outliers final: 39 residues processed: 929 average time/residue: 0.8285 time to fit residues: 1327.3996 Evaluate side-chains 845 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 806 time to evaluate : 4.884 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 39 outliers final: 1 residues processed: 39 average time/residue: 0.7069 time to fit residues: 59.0859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 440 optimal weight: 4.9990 chunk 284 optimal weight: 0.0870 chunk 424 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 452 optimal weight: 30.0000 chunk 484 optimal weight: 0.0070 chunk 351 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 559 optimal weight: 0.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN ** T 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 33 GLN V 75 GLN W 42 GLN ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 60 HIS ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 89066 Z= 0.176 Angle : 0.702 13.559 129357 Z= 0.352 Chirality : 0.039 0.353 16167 Planarity : 0.005 0.152 9565 Dihedral : 24.545 179.868 33102 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 1.54 % Allowed : 9.82 % Favored : 88.64 % Rotamer: Outliers : 1.60 % Allowed : 33.27 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.06 % 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: -1.76 (0.11), residues: 5581 helix: 0.84 (0.13), residues: 1707 sheet: -1.21 (0.17), residues: 946 loop : -2.50 (0.11), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP C 235 HIS 0.008 0.001 HIS g 295 PHE 0.040 0.002 PHE B 142 TYR 0.046 0.002 TYR I 193 ARG 0.015 0.001 ARG S 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 924 time to evaluate : 4.829 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 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: 72 outliers final: 29 residues processed: 964 average time/residue: 0.8379 time to fit residues: 1382.9487 Evaluate side-chains 867 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 838 time to evaluate : 4.746 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 29 outliers final: 1 residues processed: 29 average time/residue: 0.6858 time to fit residues: 42.3067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 647 optimal weight: 40.0000 chunk 681 optimal weight: 7.9990 chunk 621 optimal weight: 30.0000 chunk 662 optimal weight: 9.9990 chunk 398 optimal weight: 3.9990 chunk 288 optimal weight: 20.0000 chunk 520 optimal weight: 30.0000 chunk 203 optimal weight: 10.0000 chunk 598 optimal weight: 40.0000 chunk 626 optimal weight: 9.9990 chunk 660 optimal weight: 30.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 104 GLN ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 HIS ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** T 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 29 HIS ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 ASN ** Y 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 113 ASN ** Z 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 32 ASN ** g 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 274 ASN ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 HIS m 67 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 89066 Z= 0.421 Angle : 0.852 14.247 129357 Z= 0.430 Chirality : 0.045 0.342 16167 Planarity : 0.007 0.154 9565 Dihedral : 24.773 178.973 33102 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 30.69 Ramachandran Plot: Outliers : 1.54 % Allowed : 12.36 % Favored : 86.10 % Rotamer: Outliers : 1.84 % Allowed : 34.40 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.11), residues: 5581 helix: 0.43 (0.12), residues: 1704 sheet: -1.37 (0.16), residues: 958 loop : -2.63 (0.11), residues: 2919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP S 84 HIS 0.012 0.002 HIS g 295 PHE 0.069 0.003 PHE I 192 TYR 0.035 0.003 TYR I 113 ARG 0.010 0.001 ARG X 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 830 time to evaluate : 4.786 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 outliers start: 83 outliers final: 50 residues processed: 869 average time/residue: 0.8287 time to fit residues: 1237.6018 Evaluate side-chains 831 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 781 time to evaluate : 4.890 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 50 outliers final: 1 residues processed: 50 average time/residue: 0.6737 time to fit residues: 69.5973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 435 optimal weight: 1.9990 chunk 700 optimal weight: 30.0000 chunk 427 optimal weight: 0.3980 chunk 332 optimal weight: 6.9990 chunk 487 optimal weight: 7.9990 chunk 735 optimal weight: 6.9990 chunk 676 optimal weight: 6.9990 chunk 585 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 452 optimal weight: 6.9990 chunk 358 optimal weight: 0.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS B 163 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN I 88 ASN J 110 GLN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 29 HIS ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 GLN c 27 GLN g 32 ASN ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 89066 Z= 0.206 Angle : 0.742 14.057 129357 Z= 0.372 Chirality : 0.040 0.351 16167 Planarity : 0.005 0.154 9565 Dihedral : 24.631 179.854 33102 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 1.49 % Allowed : 9.71 % Favored : 88.80 % Rotamer: Outliers : 0.64 % Allowed : 34.91 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.11), residues: 5581 helix: 0.53 (0.13), residues: 1718 sheet: -1.21 (0.17), residues: 949 loop : -2.52 (0.11), residues: 2914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP N 25 HIS 0.011 0.001 HIS g 295 PHE 0.050 0.002 PHE I 192 TYR 0.046 0.002 TYR K 65 ARG 0.014 0.001 ARG F 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11162 Ramachandran restraints generated. 5581 Oldfield, 0 Emsley, 5581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 871 time to evaluate : 4.738 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 889 average time/residue: 0.8307 time to fit residues: 1266.2590 Evaluate side-chains 829 residues out of total 4838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 813 time to evaluate : 4.812 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.6585 time to fit residues: 25.6179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 465 optimal weight: 7.9990 chunk 623 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 539 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 586 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 602 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 99 HIS ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.086054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.066131 restraints weight = 387656.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.067890 restraints weight = 173279.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.068742 restraints weight = 105507.769| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 89066 Z= 0.292 Angle : 0.768 14.502 129357 Z= 0.387 Chirality : 0.041 0.348 16167 Planarity : 0.006 0.157 9565 Dihedral : 24.625 179.133 33102 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 1.47 % Allowed : 11.50 % Favored : 87.03 % Rotamer: Outliers : 0.98 % Allowed : 35.38 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.06 % 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: -1.98 (0.11), residues: 5581 helix: 0.51 (0.13), residues: 1710 sheet: -1.31 (0.17), residues: 951 loop : -2.54 (0.11), residues: 2920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP S 84 HIS 0.010 0.002 HIS g 295 PHE 0.054 0.002 PHE I 192 TYR 0.046 0.003 TYR K 12 ARG 0.020 0.001 ARG D 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22664.78 seconds wall clock time: 398 minutes 55.31 seconds (23935.31 seconds total)