Starting phenix.real_space_refine on Thu Feb 22 12:44:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mka_23888/02_2024/7mka_23888.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mka_23888/02_2024/7mka_23888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mka_23888/02_2024/7mka_23888.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mka_23888/02_2024/7mka_23888.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mka_23888/02_2024/7mka_23888.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mka_23888/02_2024/7mka_23888.pdb" } resolution = 3.54 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 871 atoms to isotropic. 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 8 6.06 5 P 95 5.49 5 Mg 2 5.21 5 S 181 5.16 5 C 20739 2.51 5 N 5818 2.21 5 O 6541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 39": "OE1" <-> "OE2" Residue "a GLU 76": "OE1" <-> "OE2" Residue "a ASP 85": "OD1" <-> "OD2" Residue "a PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 257": "NH1" <-> "NH2" Residue "a GLU 293": "OE1" <-> "OE2" Residue "a TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 500": "OE1" <-> "OE2" Residue "a ASP 526": "OD1" <-> "OD2" Residue "a ASP 592": "OD1" <-> "OD2" Residue "a GLU 593": "OE1" <-> "OE2" Residue "a ASP 602": "OD1" <-> "OD2" Residue "a PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 727": "OD1" <-> "OD2" Residue "a ARG 731": "NH1" <-> "NH2" Residue "a PHE 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 791": "OD1" <-> "OD2" Residue "a PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 833": "OE1" <-> "OE2" Residue "a GLU 846": "OE1" <-> "OE2" Residue "a TYR 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 1005": "OE1" <-> "OE2" Residue "a TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 1206": "OD1" <-> "OD2" Residue "a GLU 1256": "OE1" <-> "OE2" Residue "a GLU 1307": "OE1" <-> "OE2" Residue "a GLU 1411": "OE1" <-> "OE2" Residue "b PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 61": "OD1" <-> "OD2" Residue "b ASP 106": "OD1" <-> "OD2" Residue "b PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 183": "OE1" <-> "OE2" Residue "b TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 209": "OE1" <-> "OE2" Residue "b PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 332": "OD1" <-> "OD2" Residue "b PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 336": "NH1" <-> "NH2" Residue "b PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 398": "NH1" <-> "NH2" Residue "b PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 476": "NH1" <-> "NH2" Residue "b ASP 568": "OD1" <-> "OD2" Residue "b ARG 595": "NH1" <-> "NH2" Residue "b ARG 604": "NH1" <-> "NH2" Residue "b PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 629": "OD1" <-> "OD2" Residue "b TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 807": "NH1" <-> "NH2" Residue "b GLU 810": "OE1" <-> "OE2" Residue "b TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 872": "OE1" <-> "OE2" Residue "b GLU 924": "OE1" <-> "OE2" Residue "b GLU 945": "OE1" <-> "OE2" Residue "b PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 1190": "OD1" <-> "OD2" Residue "b TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 210": "OE1" <-> "OE2" Residue "c PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 124": "OE1" <-> "OE2" Residue "e GLU 6": "OE1" <-> "OE2" Residue "e GLU 40": "OE1" <-> "OE2" Residue "e ASP 41": "OD1" <-> "OD2" Residue "e PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 169": "NH1" <-> "NH2" Residue "f TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 119": "NH1" <-> "NH2" Residue "f ASP 145": "OD1" <-> "OD2" Residue "f GLU 149": "OE1" <-> "OE2" Residue "g PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 6": "OD1" <-> "OD2" Residue "g TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 118": "OD1" <-> "OD2" Residue "g ASP 135": "OD1" <-> "OD2" Residue "h GLU 27": "OE1" <-> "OE2" Residue "h GLU 106": "OE1" <-> "OE2" Residue "i ARG 30": "NH1" <-> "NH2" Residue "i ASP 72": "OD1" <-> "OD2" Residue "i PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 32": "OE1" <-> "OE2" Residue "j TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 36": "OE1" <-> "OE2" Residue "k PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 33": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33384 Number of models: 1 Model: "" Number of chains: 21 Chain: "N" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 798 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "O" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 821 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "a" Number of atoms: 11189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1425, 11189 Classifications: {'peptide': 1425} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 65, 'TRANS': 1355} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "b" Number of atoms: 9197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1160, 9197 Classifications: {'peptide': 1160} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 5} Link IDs: {'CIS': 12, 'PCIS': 2, 'PTRANS': 49, 'TRANS': 1096} Chain breaks: 8 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "c" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "d" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1331 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "e" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "f" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "g" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "h" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 2 Chain: "i" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "j" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "k" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "l" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "r" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 4, 'rna3p_pyr': 7} Link IDs: {'rna2p': 4, 'rna3p': 11} Chain: "a" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2459 SG CYS a 110 118.522 92.122 101.095 1.00216.77 S ATOM 2764 SG CYS a 148 118.359 90.034 104.145 1.00265.00 S ATOM 2902 SG CYS a 167 118.716 93.328 103.507 1.00271.97 S ATOM 2130 SG CYS a 67 101.242 103.924 55.935 1.00242.80 S ATOM 2152 SG CYS a 70 102.931 104.297 54.678 1.00263.01 S ATOM 21530 SG CYS b1163 112.630 92.713 62.884 1.00771.81 S ATOM 21548 SG CYS b1166 111.149 94.815 65.698 1.00731.01 S ATOM 21673 SG CYS b1182 111.818 96.553 62.930 1.00879.94 S ATOM 21692 SG CYS b1185 113.979 94.998 65.968 1.00908.11 S ATOM 22652 SG CYS c 86 44.460 94.148 18.041 1.00652.87 S ATOM 22669 SG CYS c 88 46.148 96.993 19.675 1.00684.17 S ATOM 22702 SG CYS c 92 42.913 97.678 17.810 1.00633.55 S ATOM 22725 SG CYS c 95 43.260 95.914 21.310 1.00603.63 S ATOM 30351 SG CYS i 7 60.869 90.821 144.402 1.00606.34 S ATOM 30376 SG CYS i 10 62.575 93.140 141.777 1.00604.81 S ATOM 30542 SG CYS i 29 64.284 89.954 142.971 1.00592.83 S ATOM 30566 SG CYS i 32 63.719 92.765 145.451 1.00615.85 S ATOM 30893 SG CYS i 75 26.711 66.210 121.024 1.00999.99 S ATOM 30915 SG CYS i 78 25.148 68.332 122.861 1.00999.99 S ATOM 31131 SG CYS i 103 26.638 69.766 119.530 1.00999.99 S ATOM 31151 SG CYS i 106 28.924 69.043 122.571 1.00999.99 S ATOM 31279 SG CYS j 7 30.918 83.427 48.516 1.00416.77 S ATOM 31302 SG CYS j 10 29.679 82.471 45.179 1.00474.02 S ATOM 31582 SG CYS j 45 28.733 79.949 47.886 1.00511.53 S ATOM 31588 SG CYS j 46 27.217 83.208 47.010 1.00497.40 S ATOM 32732 SG CYS l 31 43.970 125.547 56.097 1.00283.35 S ATOM 32752 SG CYS l 34 40.854 127.102 55.926 1.00331.71 S ATOM 32856 SG CYS l 48 44.100 129.192 55.782 1.00280.24 S ATOM 32879 SG CYS l 51 42.245 127.713 59.026 1.00298.71 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN a1801 " occ=0.95 Time building chain proxies: 16.57, per 1000 atoms: 0.50 Number of scatterers: 33384 At special positions: 0 Unit cell: (170.64, 163.08, 164.16, 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 8 29.99 S 181 16.00 P 95 15.00 Mg 2 11.99 O 6541 8.00 N 5818 7.00 C 20739 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: 14.01 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a1801 " pdb="ZN ZN a1801 " - pdb=" SG CYS a 167 " pdb="ZN ZN a1801 " - pdb=" SG CYS a 148 " pdb="ZN ZN a1801 " - pdb=" SG CYS a 110 " pdb=" ZN a1802 " pdb="ZN ZN a1802 " - pdb=" SG CYS a 67 " pdb="ZN ZN a1802 " - pdb=" SG CYS a 70 " pdb="ZN ZN a1802 " - pdb=" NE2 HIS a 80 " pdb=" ZN b1301 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1166 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1185 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1182 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1163 " pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 88 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 95 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 92 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 86 " pdb=" ZN i 201 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 32 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 29 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 7 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 10 " pdb=" ZN i 202 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 78 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 75 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 106 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 103 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 10 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 46 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 45 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 7 " pdb=" ZN l 101 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 34 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 31 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 48 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 51 " Number of angles added : 36 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7440 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 42 sheets defined 37.3% alpha, 14.9% beta 29 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 10.25 Creating SS restraints... Processing helix chain 'a' and resid 23 through 31 Processing helix chain 'a' and resid 92 through 95 Processing helix chain 'a' and resid 96 through 105 Processing helix chain 'a' and resid 120 through 128 Processing helix chain 'a' and resid 132 through 142 Processing helix chain 'a' and resid 191 through 195 Processing helix chain 'a' and resid 203 through 214 Processing helix chain 'a' and resid 215 through 222 removed outlier: 3.715A pdb=" N PHE a 219 " --> pdb=" O SER a 215 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR a 220 " --> pdb=" O VAL a 216 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 235 removed outlier: 3.581A pdb=" N ILE a 235 " --> pdb=" O GLU a 232 " (cutoff:3.500A) Processing helix chain 'a' and resid 243 through 247 removed outlier: 3.551A pdb=" N VAL a 246 " --> pdb=" O PRO a 243 " (cutoff:3.500A) Processing helix chain 'a' and resid 260 through 282 removed outlier: 3.528A pdb=" N PHE a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 288 through 305 Processing helix chain 'a' and resid 324 through 330 Processing helix chain 'a' and resid 368 through 374 Processing helix chain 'a' and resid 384 through 395 Processing helix chain 'a' and resid 471 through 473 No H-bonds generated for 'chain 'a' and resid 471 through 473' Processing helix chain 'a' and resid 474 through 479 removed outlier: 3.633A pdb=" N TYR a 478 " --> pdb=" O VAL a 474 " (cutoff:3.500A) Processing helix chain 'a' and resid 494 through 502 Processing helix chain 'a' and resid 506 through 510 Processing helix chain 'a' and resid 524 through 535 Processing helix chain 'a' and resid 542 through 553 Processing helix chain 'a' and resid 573 through 581 removed outlier: 3.929A pdb=" N VAL a 580 " --> pdb=" O GLN a 576 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA a 581 " --> pdb=" O ILE a 577 " (cutoff:3.500A) Processing helix chain 'a' and resid 618 through 623 Processing helix chain 'a' and resid 628 through 637 Processing helix chain 'a' and resid 640 through 661 removed outlier: 3.933A pdb=" N LYS a 644 " --> pdb=" O GLN a 640 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE a 655 " --> pdb=" O LYS a 651 " (cutoff:3.500A) Processing helix chain 'a' and resid 665 through 669 Processing helix chain 'a' and resid 672 through 699 Processing helix chain 'a' and resid 709 through 737 Processing helix chain 'a' and resid 741 through 749 removed outlier: 3.903A pdb=" N GLN a 745 " --> pdb=" O ASN a 741 " (cutoff:3.500A) Processing helix chain 'a' and resid 754 through 763 Processing helix chain 'a' and resid 809 through 843 removed outlier: 4.724A pdb=" N ALA a 832 " --> pdb=" O ALA a 828 " (cutoff:3.500A) Processing helix chain 'a' and resid 867 through 871 Processing helix chain 'a' and resid 889 through 898 Processing helix chain 'a' and resid 909 through 913 Processing helix chain 'a' and resid 922 through 947 Processing helix chain 'a' and resid 960 through 970 Processing helix chain 'a' and resid 982 through 997 removed outlier: 4.200A pdb=" N LYS a 991 " --> pdb=" O VAL a 987 " (cutoff:3.500A) Processing helix chain 'a' and resid 1004 through 1015 removed outlier: 3.627A pdb=" N GLN a1008 " --> pdb=" O ASN a1004 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL a1015 " --> pdb=" O GLN a1011 " (cutoff:3.500A) Processing helix chain 'a' and resid 1015 through 1026 Processing helix chain 'a' and resid 1027 through 1034 Processing helix chain 'a' and resid 1038 through 1056 Processing helix chain 'a' and resid 1063 through 1078 Proline residue: a1075 - end of helix removed outlier: 3.902A pdb=" N GLN a1078 " --> pdb=" O GLU a1074 " (cutoff:3.500A) Processing helix chain 'a' and resid 1096 through 1106 Processing helix chain 'a' and resid 1127 through 1139 Processing helix chain 'a' and resid 1142 through 1146 removed outlier: 3.568A pdb=" N VAL a1146 " --> pdb=" O THR a1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1142 through 1146' Processing helix chain 'a' and resid 1167 through 1173 Processing helix chain 'a' and resid 1198 through 1205 Processing helix chain 'a' and resid 1208 through 1220 removed outlier: 3.746A pdb=" N PHE a1220 " --> pdb=" O ILE a1216 " (cutoff:3.500A) Processing helix chain 'a' and resid 1255 through 1269 removed outlier: 3.511A pdb=" N MET a1259 " --> pdb=" O GLU a1255 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU a1269 " --> pdb=" O ASN a1265 " (cutoff:3.500A) Processing helix chain 'a' and resid 1315 through 1319 Processing helix chain 'a' and resid 1331 through 1339 Processing helix chain 'a' and resid 1340 through 1358 Processing helix chain 'a' and resid 1364 through 1377 removed outlier: 4.114A pdb=" N MET a1368 " --> pdb=" O ASN a1364 " (cutoff:3.500A) Processing helix chain 'a' and resid 1395 through 1401 removed outlier: 3.823A pdb=" N ARG a1399 " --> pdb=" O GLY a1395 " (cutoff:3.500A) Processing helix chain 'a' and resid 1406 through 1416 Processing helix chain 'a' and resid 1423 through 1431 Processing helix chain 'a' and resid 1436 through 1441 removed outlier: 4.049A pdb=" N PHE a1441 " --> pdb=" O THR a1438 " (cutoff:3.500A) Processing helix chain 'a' and resid 1447 through 1453 Processing helix chain 'b' and resid 27 through 29 No H-bonds generated for 'chain 'b' and resid 27 through 29' Processing helix chain 'b' and resid 30 through 42 removed outlier: 3.872A pdb=" N ILE b 34 " --> pdb=" O SER b 30 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER b 35 " --> pdb=" O TRP b 31 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA b 36 " --> pdb=" O ALA b 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 57 removed outlier: 3.629A pdb=" N PHE b 51 " --> pdb=" O GLN b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 66 removed outlier: 4.153A pdb=" N ASP b 66 " --> pdb=" O ILE b 62 " (cutoff:3.500A) Processing helix chain 'b' and resid 113 through 121 Processing helix chain 'b' and resid 179 through 184 Processing helix chain 'b' and resid 185 through 192 Processing helix chain 'b' and resid 246 through 250 removed outlier: 3.515A pdb=" N PHE b 250 " --> pdb=" O GLY b 247 " (cutoff:3.500A) Processing helix chain 'b' and resid 282 through 290 Processing helix chain 'b' and resid 293 through 302 removed outlier: 3.627A pdb=" N ILE b 297 " --> pdb=" O PRO b 293 " (cutoff:3.500A) Processing helix chain 'b' and resid 308 through 321 Proline residue: b 316 - end of helix removed outlier: 3.583A pdb=" N GLY b 321 " --> pdb=" O CYS b 317 " (cutoff:3.500A) Processing helix chain 'b' and resid 322 through 324 No H-bonds generated for 'chain 'b' and resid 322 through 324' Processing helix chain 'b' and resid 326 through 333 Processing helix chain 'b' and resid 348 through 359 Processing helix chain 'b' and resid 370 through 390 Processing helix chain 'b' and resid 408 through 430 removed outlier: 3.900A pdb=" N LEU b 416 " --> pdb=" O LEU b 412 " (cutoff:3.500A) Processing helix chain 'b' and resid 444 through 464 removed outlier: 4.250A pdb=" N ILE b 448 " --> pdb=" O MET b 444 " (cutoff:3.500A) Processing helix chain 'b' and resid 487 through 496 removed outlier: 3.878A pdb=" N ARG b 496 " --> pdb=" O LEU b 492 " (cutoff:3.500A) Processing helix chain 'b' and resid 515 through 519 Processing helix chain 'b' and resid 551 through 561 removed outlier: 3.825A pdb=" N ILE b 555 " --> pdb=" O PRO b 551 " (cutoff:3.500A) Processing helix chain 'b' and resid 565 through 569 Processing helix chain 'b' and resid 592 through 606 removed outlier: 3.943A pdb=" N LEU b 596 " --> pdb=" O ASN b 592 " (cutoff:3.500A) Processing helix chain 'b' and resid 654 through 668 removed outlier: 3.629A pdb=" N ILE b 658 " --> pdb=" O ARG b 654 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP b 668 " --> pdb=" O THR b 664 " (cutoff:3.500A) Processing helix chain 'b' and resid 680 through 688 removed outlier: 3.523A pdb=" N GLY b 688 " --> pdb=" O LEU b 684 " (cutoff:3.500A) Processing helix chain 'b' and resid 695 through 699 removed outlier: 4.143A pdb=" N GLU b 699 " --> pdb=" O ALA b 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 695 through 699' Processing helix chain 'b' and resid 744 through 749 Processing helix chain 'b' and resid 750 through 756 removed outlier: 4.071A pdb=" N ILE b 755 " --> pdb=" O VAL b 751 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE b 756 " --> pdb=" O ALA b 752 " (cutoff:3.500A) Processing helix chain 'b' and resid 758 through 762 Processing helix chain 'b' and resid 763 through 775 removed outlier: 4.131A pdb=" N LYS b 775 " --> pdb=" O SER b 771 " (cutoff:3.500A) Processing helix chain 'b' and resid 807 through 812 Processing helix chain 'b' and resid 843 through 849 Processing helix chain 'b' and resid 889 through 893 removed outlier: 3.585A pdb=" N LYS b 892 " --> pdb=" O THR b 889 " (cutoff:3.500A) Processing helix chain 'b' and resid 995 through 999 Processing helix chain 'b' and resid 1014 through 1017 Processing helix chain 'b' and resid 1023 through 1039 Processing helix chain 'b' and resid 1051 through 1063 removed outlier: 3.517A pdb=" N ILE b1055 " --> pdb=" O THR b1051 " (cutoff:3.500A) Processing helix chain 'b' and resid 1099 through 1103 Processing helix chain 'b' and resid 1131 through 1142 Processing helix chain 'b' and resid 1143 through 1153 Processing helix chain 'b' and resid 1197 through 1210 Processing helix chain 'c' and resid 26 through 40 Processing helix chain 'c' and resid 59 through 68 Processing helix chain 'c' and resid 76 through 80 Processing helix chain 'c' and resid 92 through 96 removed outlier: 3.696A pdb=" N SER c 96 " --> pdb=" O ASP c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 114 through 118 removed outlier: 3.525A pdb=" N LEU c 118 " --> pdb=" O SER c 115 " (cutoff:3.500A) Processing helix chain 'c' and resid 167 through 171 Processing helix chain 'c' and resid 204 through 209 Processing helix chain 'c' and resid 239 through 266 Processing helix chain 'd' and resid 51 through 75 removed outlier: 3.582A pdb=" N ALA d 55 " --> pdb=" O ASN d 51 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG d 56 " --> pdb=" O LEU d 52 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU d 57 " --> pdb=" O SER d 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS d 75 " --> pdb=" O LYS d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 118 through 134 removed outlier: 4.145A pdb=" N THR d 133 " --> pdb=" O LEU d 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 138 through 152 removed outlier: 4.306A pdb=" N ASN d 150 " --> pdb=" O GLN d 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 171 removed outlier: 3.842A pdb=" N SER d 169 " --> pdb=" O GLN d 165 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR d 170 " --> pdb=" O LEU d 166 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 179 removed outlier: 4.060A pdb=" N VAL d 177 " --> pdb=" O HIS d 173 " (cutoff:3.500A) Processing helix chain 'd' and resid 180 through 183 removed outlier: 4.012A pdb=" N LEU d 183 " --> pdb=" O LEU d 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 180 through 183' Processing helix chain 'd' and resid 187 through 195 removed outlier: 4.166A pdb=" N ALA d 191 " --> pdb=" O THR d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 202 removed outlier: 4.044A pdb=" N ASN d 199 " --> pdb=" O ILE d 195 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE d 202 " --> pdb=" O LEU d 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 216 removed outlier: 4.588A pdb=" N GLU d 213 " --> pdb=" O ARG d 209 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU d 214 " --> pdb=" O ILE d 210 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN d 216 " --> pdb=" O LYS d 212 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 26 removed outlier: 4.389A pdb=" N ARG e 7 " --> pdb=" O GLN e 3 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 36 removed outlier: 3.540A pdb=" N VAL e 35 " --> pdb=" O THR e 31 " (cutoff:3.500A) Processing helix chain 'e' and resid 38 through 47 Processing helix chain 'e' and resid 65 through 72 Processing helix chain 'e' and resid 89 through 104 Processing helix chain 'e' and resid 117 through 122 Processing helix chain 'e' and resid 157 through 169 Processing helix chain 'e' and resid 182 through 189 Processing helix chain 'f' and resid 86 through 103 Processing helix chain 'f' and resid 116 through 128 Processing helix chain 'g' and resid 14 through 18 Processing helix chain 'g' and resid 21 through 35 Processing helix chain 'i' and resid 61 through 65 removed outlier: 3.710A pdb=" N ASP i 65 " --> pdb=" O ILE i 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 17 through 28 Processing helix chain 'j' and resid 31 through 40 Processing helix chain 'j' and resid 43 through 52 removed outlier: 3.813A pdb=" N ARG j 47 " --> pdb=" O ARG j 43 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N MET j 49 " --> pdb=" O CYS j 45 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE j 50 " --> pdb=" O CYS j 46 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 62 Processing helix chain 'k' and resid 6 through 10 removed outlier: 3.548A pdb=" N LEU k 9 " --> pdb=" O ARG k 6 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 52 removed outlier: 3.684A pdb=" N GLY k 43 " --> pdb=" O ASP k 39 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU k 45 " --> pdb=" O THR k 41 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN k 52 " --> pdb=" O ALA k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 112 Processing sheet with id=AA1, first strand: chain 'a' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'a' and resid 82 through 83 removed outlier: 3.769A pdb=" N GLY a 82 " --> pdb=" O VAL a 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 106 through 107 Processing sheet with id=AA4, first strand: chain 'a' and resid 173 through 177 Processing sheet with id=AA5, first strand: chain 'a' and resid 343 through 344 Processing sheet with id=AA6, first strand: chain 'a' and resid 455 through 458 removed outlier: 3.559A pdb=" N MET a 487 " --> pdb=" O THR a 351 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR a 351 " --> pdb=" O MET a 487 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA a 349 " --> pdb=" O LEU a 489 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N PHE a 468 " --> pdb=" O ARG a 350 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL a 352 " --> pdb=" O PHE a 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 455 through 458 removed outlier: 3.559A pdb=" N MET a 487 " --> pdb=" O THR a 351 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR a 351 " --> pdb=" O MET a 487 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA a 349 " --> pdb=" O LEU a 489 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 365 through 367 removed outlier: 5.629A pdb=" N VAL a 366 " --> pdb=" O ILE a 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'a' and resid 376 through 379 removed outlier: 3.522A pdb=" N VAL a 432 " --> pdb=" O GLU a 378 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL a 405 " --> pdb=" O ILE a 413 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 512 through 513 removed outlier: 3.724A pdb=" N LYS a 518 " --> pdb=" O SER a 513 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 587 through 589 removed outlier: 3.548A pdb=" N LEU a 588 " --> pdb=" O ILE a 607 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 849 through 850 removed outlier: 6.967A pdb=" N THR a 856 " --> pdb=" O ILE a 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 1283 through 1292 removed outlier: 3.541A pdb=" N MET a1285 " --> pdb=" O VAL a1305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 1224 through 1228 removed outlier: 4.066A pdb=" N LEU a1236 " --> pdb=" O LEU a1197 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL a1242 " --> pdb=" O TRP a1191 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP a1191 " --> pdb=" O VAL a1242 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA a1149 " --> pdb=" O GLU a1196 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER a1150 " --> pdb=" O ARG i 45 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ARG i 45 " --> pdb=" O SER a1150 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE a1152 " --> pdb=" O VAL i 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 143 through 147 removed outlier: 5.608A pdb=" N VAL a1443 " --> pdb=" O ILE g 61 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY g 59 " --> pdb=" O ILE a1445 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'f' and resid 143 through 147 removed outlier: 5.608A pdb=" N VAL a1443 " --> pdb=" O ILE g 61 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY g 59 " --> pdb=" O ILE a1445 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE g 79 " --> pdb=" O ILE g 45 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE g 45 " --> pdb=" O PHE g 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 69 through 73 removed outlier: 3.548A pdb=" N GLY b 93 " --> pdb=" O ASP b 131 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP b 131 " --> pdb=" O GLY b 93 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE b 95 " --> pdb=" O PHE b 129 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE b 129 " --> pdb=" O ILE b 95 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL b 97 " --> pdb=" O GLY b 127 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY b 127 " --> pdb=" O VAL b 97 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER b 126 " --> pdb=" O ARG b 169 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG b 169 " --> pdb=" O SER b 126 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU b 128 " --> pdb=" O ILE b 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 101 through 103 removed outlier: 3.986A pdb=" N VAL b 102 " --> pdb=" O HIS b 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 203 through 204 Processing sheet with id=AC2, first strand: chain 'b' and resid 404 through 407 Processing sheet with id=AC3, first strand: chain 'b' and resid 224 through 227 removed outlier: 4.277A pdb=" N HIS b 236 " --> pdb=" O LEU b 258 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU b 258 " --> pdb=" O HIS b 236 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE b 240 " --> pdb=" O LEU b 254 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN b 255 " --> pdb=" O THR b 272 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR b 268 " --> pdb=" O TYR b 259 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE b 269 " --> pdb=" O ILE b 280 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE b 280 " --> pdb=" O ILE b 269 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA b 271 " --> pdb=" O GLN b 278 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN b 278 " --> pdb=" O ALA b 271 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU b 273 " --> pdb=" O ILE b 276 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 544 through 545 Processing sheet with id=AC5, first strand: chain 'b' and resid 650 through 651 removed outlier: 3.546A pdb=" N GLU b 650 " --> pdb=" O GLU b 641 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 585 through 590 removed outlier: 3.683A pdb=" N HIS b 587 " --> pdb=" O VAL b 580 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL b 580 " --> pdb=" O HIS b 587 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL b 589 " --> pdb=" O THR b 578 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR b 578 " --> pdb=" O VAL b 589 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b' and resid 792 through 796 removed outlier: 3.702A pdb=" N ILE b 795 " --> pdb=" O LEU b 854 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG b 857 " --> pdb=" O VAL b 968 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL b 966 " --> pdb=" O TYR b 859 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP b 861 " --> pdb=" O VAL b 964 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG b 967 " --> pdb=" O GLN b 951 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLN b 951 " --> pdb=" O ARG b 967 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG b 969 " --> pdb=" O VAL b 949 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL b 949 " --> pdb=" O ARG b 969 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 978 through 981 removed outlier: 5.451A pdb=" N LYS b 979 " --> pdb=" O LEU b1095 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU b1095 " --> pdb=" O LYS b 979 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA b 981 " --> pdb=" O GLN b1093 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE b1086 " --> pdb=" O ILE b 827 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE b 827 " --> pdb=" O PHE b1086 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LEU b1010 " --> pdb=" O ASN b 822 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE b 824 " --> pdb=" O LEU b1010 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE b1012 " --> pdb=" O ILE b 824 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA b 826 " --> pdb=" O ILE b1012 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N MET b 839 " --> pdb=" O GLY b 991 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR b 993 " --> pdb=" O MET b 839 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N MET b 841 " --> pdb=" O THR b 993 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 978 through 981 removed outlier: 5.451A pdb=" N LYS b 979 " --> pdb=" O LEU b1095 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU b1095 " --> pdb=" O LYS b 979 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA b 981 " --> pdb=" O GLN b1093 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 910 through 912 removed outlier: 6.819A pdb=" N THR b 939 " --> pdb=" O ILE b 911 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 1158 through 1162 Processing sheet with id=AD3, first strand: chain 'c' and resid 8 through 13 removed outlier: 6.609A pdb=" N ASP c 19 " --> pdb=" O ARG c 11 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA c 13 " --> pdb=" O ASN c 17 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN c 17 " --> pdb=" O ALA c 13 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE c 20 " --> pdb=" O MET c 230 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N MET c 230 " --> pdb=" O PHE c 20 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 119 through 120 removed outlier: 5.649A pdb=" N LYS c 160 " --> pdb=" O ILE c 46 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE c 46 " --> pdb=" O LYS c 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE l 67 " --> pdb=" O VAL c 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'c' and resid 72 through 74 removed outlier: 4.238A pdb=" N HIS c 131 " --> pdb=" O GLN c 73 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'c' and resid 111 through 112 Processing sheet with id=AD7, first strand: chain 'd' and resid 36 through 37 Processing sheet with id=AD8, first strand: chain 'e' and resid 60 through 62 removed outlier: 7.127A pdb=" N TRP e 79 " --> pdb=" O ILE e 109 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N VAL e 111 " --> pdb=" O TRP e 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'e' and resid 152 through 154 removed outlier: 3.761A pdb=" N LYS e 152 " --> pdb=" O ILE e 199 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE e 199 " --> pdb=" O LYS e 152 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'e' and resid 152 through 154 removed outlier: 3.761A pdb=" N LYS e 152 " --> pdb=" O ILE e 199 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE e 199 " --> pdb=" O LYS e 152 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'g' and resid 143 through 147 removed outlier: 3.682A pdb=" N VAL g 92 " --> pdb=" O GLU g 100 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLU g 100 " --> pdb=" O VAL g 92 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS g 107 " --> pdb=" O ALA g 159 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'h' and resid 95 through 98 removed outlier: 4.290A pdb=" N TYR h 95 " --> pdb=" O ILE h 144 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE h 144 " --> pdb=" O TYR h 95 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU h 27 " --> pdb=" O SER h 13 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL h 15 " --> pdb=" O ARG h 25 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG h 25 " --> pdb=" O VAL h 15 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU h 122 " --> pdb=" O ASP h 41 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR h 116 " --> pdb=" O MET h 123 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU h 125 " --> pdb=" O VAL h 114 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL h 114 " --> pdb=" O LEU h 125 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU h 111 " --> pdb=" O GLU h 106 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLU h 106 " --> pdb=" O LEU h 111 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA h 113 " --> pdb=" O PHE h 104 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE h 104 " --> pdb=" O ALA h 113 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR h 115 " --> pdb=" O TYR h 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'i' and resid 14 through 18 Processing sheet with id=AE5, first strand: chain 'i' and resid 84 through 87 Processing sheet with id=AE6, first strand: chain 'k' and resid 19 through 24 removed outlier: 4.534A pdb=" N ALA k 30 " --> pdb=" O ASP k 24 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE k 71 " --> pdb=" O PHE k 35 " (cutoff:3.500A) 1215 hydrogen bonds defined for protein. 3336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 14.80 Time building geometry restraints manager: 15.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10155 1.33 - 1.45: 5894 1.45 - 1.57: 17652 1.57 - 1.70: 176 1.70 - 1.82: 290 Bond restraints: 34167 Sorted by residual: bond pdb=" C CYS b 523 " pdb=" N PRO b 524 " ideal model delta sigma weight residual 1.334 1.304 0.029 8.40e-03 1.42e+04 1.20e+01 bond pdb=" O3' A r 46 " pdb=" P U r 47 " ideal model delta sigma weight residual 1.607 1.556 0.051 1.50e-02 4.44e+03 1.17e+01 bond pdb=" O3' DA O -47 " pdb=" P DT O -46 " ideal model delta sigma weight residual 1.607 1.557 0.050 1.50e-02 4.44e+03 1.10e+01 bond pdb=" C MET a1433 " pdb=" N ALA a1434 " ideal model delta sigma weight residual 1.329 1.269 0.060 1.86e-02 2.89e+03 1.03e+01 bond pdb=" O3' U r 42 " pdb=" P A r 43 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.50e-02 4.44e+03 1.02e+01 ... (remaining 34162 not shown) Histogram of bond angle deviations from ideal: 96.09 - 103.68: 707 103.68 - 111.28: 14736 111.28 - 118.87: 13097 118.87 - 126.46: 17355 126.46 - 134.05: 650 Bond angle restraints: 46545 Sorted by residual: angle pdb=" O3' U r 40 " pdb=" C3' U r 40 " pdb=" C2' U r 40 " ideal model delta sigma weight residual 113.70 101.03 12.67 1.50e+00 4.44e-01 7.14e+01 angle pdb=" O2' U r 47 " pdb=" C2' U r 47 " pdb=" C1' U r 47 " ideal model delta sigma weight residual 108.40 96.09 12.31 1.50e+00 4.44e-01 6.73e+01 angle pdb=" O3' DG O -39 " pdb=" C3' DG O -39 " pdb=" C2' DG O -39 " ideal model delta sigma weight residual 111.50 99.45 12.05 1.50e+00 4.44e-01 6.46e+01 angle pdb=" N MET b1210 " pdb=" CA MET b1210 " pdb=" C MET b1210 " ideal model delta sigma weight residual 113.20 106.30 6.90 1.21e+00 6.83e-01 3.26e+01 angle pdb=" C ASN a 253 " pdb=" N GLU a 254 " pdb=" CA GLU a 254 " ideal model delta sigma weight residual 121.90 115.23 6.67 1.26e+00 6.30e-01 2.80e+01 ... (remaining 46540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 19936 35.09 - 70.18: 740 70.18 - 105.27: 48 105.27 - 140.36: 4 140.36 - 175.45: 2 Dihedral angle restraints: 20730 sinusoidal: 9238 harmonic: 11492 Sorted by residual: dihedral pdb=" CA ILE g 56 " pdb=" C ILE g 56 " pdb=" N GLN g 57 " pdb=" CA GLN g 57 " ideal model delta harmonic sigma weight residual 180.00 -144.21 -35.79 0 5.00e+00 4.00e-02 5.12e+01 dihedral pdb=" CA MET b 868 " pdb=" C MET b 868 " pdb=" N SER b 869 " pdb=" CA SER b 869 " ideal model delta harmonic sigma weight residual 180.00 -146.11 -33.89 0 5.00e+00 4.00e-02 4.59e+01 dihedral pdb=" CA ASP a 55 " pdb=" C ASP a 55 " pdb=" N PRO a 56 " pdb=" CA PRO a 56 " ideal model delta harmonic sigma weight residual 180.00 146.43 33.57 0 5.00e+00 4.00e-02 4.51e+01 ... (remaining 20727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 5049 0.106 - 0.212: 193 0.212 - 0.318: 2 0.318 - 0.424: 2 0.424 - 0.530: 1 Chirality restraints: 5247 Sorted by residual: chirality pdb=" C2' U r 40 " pdb=" C3' U r 40 " pdb=" O2' U r 40 " pdb=" C1' U r 40 " both_signs ideal model delta sigma weight residual False -2.75 -2.22 -0.53 2.00e-01 2.50e+01 7.03e+00 chirality pdb=" C3' DA O -42 " pdb=" C4' DA O -42 " pdb=" O3' DA O -42 " pdb=" C2' DA O -42 " both_signs ideal model delta sigma weight residual False -2.66 -2.30 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C3' DG O -39 " pdb=" C4' DG O -39 " pdb=" O3' DG O -39 " pdb=" C2' DG O -39 " both_signs ideal model delta sigma weight residual False -2.66 -2.99 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 5244 not shown) Planarity restraints: 5704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U r 40 " 0.035 2.00e-02 2.50e+03 2.05e-02 9.49e+00 pdb=" N1 U r 40 " -0.049 2.00e-02 2.50e+03 pdb=" C2 U r 40 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U r 40 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U r 40 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U r 40 " 0.012 2.00e-02 2.50e+03 pdb=" O4 U r 40 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U r 40 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U r 40 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C r 39 " 0.043 2.00e-02 2.50e+03 1.99e-02 8.91e+00 pdb=" N1 C r 39 " -0.015 2.00e-02 2.50e+03 pdb=" C2 C r 39 " -0.007 2.00e-02 2.50e+03 pdb=" O2 C r 39 " -0.016 2.00e-02 2.50e+03 pdb=" N3 C r 39 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C r 39 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C r 39 " 0.024 2.00e-02 2.50e+03 pdb=" C5 C r 39 " -0.014 2.00e-02 2.50e+03 pdb=" C6 C r 39 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS k 102 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C LYS k 102 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS k 102 " -0.016 2.00e-02 2.50e+03 pdb=" N THR k 103 " -0.014 2.00e-02 2.50e+03 ... (remaining 5701 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 428 2.49 - 3.09: 26864 3.09 - 3.70: 55801 3.70 - 4.30: 74493 4.30 - 4.90: 114357 Nonbonded interactions: 271943 Sorted by model distance: nonbonded pdb=" O CYS a 67 " pdb="ZN ZN a1802 " model vdw 1.888 2.230 nonbonded pdb=" OD2 ASP a 481 " pdb="MG MG a1803 " model vdw 1.934 2.170 nonbonded pdb=" OP2 C r 48 " pdb="MG MG a1803 " model vdw 1.985 2.170 nonbonded pdb=" N THR a1394 " pdb="MG MG a1804 " model vdw 2.016 2.250 nonbonded pdb=" O ILE h 144 " pdb=" NH1 ARG h 145 " model vdw 2.056 2.520 ... (remaining 271938 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=0.95 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.030 Extract box with map and model: 4.280 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 96.480 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6017 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 : 0.006 0.062 34167 Z= 0.367 Angle : 0.857 14.895 46545 Z= 0.502 Chirality : 0.048 0.530 5247 Planarity : 0.004 0.053 5704 Dihedral : 17.387 175.454 13290 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 24.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.40 % Favored : 87.58 % Rotamer: Outliers : 0.06 % Allowed : 0.55 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % Twisted General : 0.11 % 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: -1.96 (0.13), residues: 3912 helix: 0.11 (0.15), residues: 1246 sheet: -1.39 (0.21), residues: 582 loop : -2.23 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP b 466 HIS 0.009 0.001 HIS a 659 PHE 0.028 0.002 PHE d 151 TYR 0.022 0.002 TYR b 833 ARG 0.014 0.001 ARG h 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 572 time to evaluate : 3.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 225 ASN cc_start: 0.8727 (t0) cc_final: 0.8307 (t0) REVERT: a 229 SER cc_start: 0.9345 (t) cc_final: 0.8894 (p) REVERT: a 234 MET cc_start: 0.9230 (tpt) cc_final: 0.8680 (tpt) REVERT: a 236 LEU cc_start: 0.9308 (mt) cc_final: 0.9011 (mt) REVERT: a 260 ASP cc_start: 0.8255 (m-30) cc_final: 0.7913 (m-30) REVERT: a 266 LEU cc_start: 0.9491 (mt) cc_final: 0.9219 (tt) REVERT: a 444 PHE cc_start: 0.8161 (t80) cc_final: 0.7674 (t80) REVERT: a 455 MET cc_start: 0.7837 (pmm) cc_final: 0.7406 (pmm) REVERT: a 456 MET cc_start: 0.8688 (mpp) cc_final: 0.7965 (mpp) REVERT: a 478 TYR cc_start: 0.8378 (m-80) cc_final: 0.7418 (m-80) REVERT: a 495 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8607 (mm-30) REVERT: a 515 GLN cc_start: 0.9338 (tm-30) cc_final: 0.8781 (tm-30) REVERT: a 605 MET cc_start: 0.6457 (tpp) cc_final: 0.6124 (tpp) REVERT: a 662 PHE cc_start: 0.7415 (t80) cc_final: 0.6880 (t80) REVERT: a 826 ASP cc_start: 0.8908 (t70) cc_final: 0.8669 (t70) REVERT: a 852 TYR cc_start: 0.7266 (m-10) cc_final: 0.7045 (m-10) REVERT: a 994 GLN cc_start: 0.8089 (pt0) cc_final: 0.7630 (tt0) REVERT: a 1037 LEU cc_start: 0.5070 (mm) cc_final: 0.3961 (tp) REVERT: a 1074 GLU cc_start: 0.8230 (tt0) cc_final: 0.7471 (tt0) REVERT: a 1317 MET cc_start: 0.8714 (tmm) cc_final: 0.8423 (tmm) REVERT: a 1430 LEU cc_start: 0.8746 (tp) cc_final: 0.8051 (tp) REVERT: a 1454 MET cc_start: 0.6344 (mpp) cc_final: 0.5766 (mpp) REVERT: b 181 LEU cc_start: 0.9208 (mt) cc_final: 0.8952 (tp) REVERT: b 310 MET cc_start: 0.9191 (pmm) cc_final: 0.8923 (pmm) REVERT: b 391 ASP cc_start: 0.9470 (m-30) cc_final: 0.8977 (t0) REVERT: b 412 LEU cc_start: 0.9119 (mt) cc_final: 0.8837 (mt) REVERT: b 514 LEU cc_start: 0.9248 (tp) cc_final: 0.8846 (tp) REVERT: b 541 LEU cc_start: 0.9397 (pp) cc_final: 0.8896 (mp) REVERT: b 597 MET cc_start: 0.9137 (tpp) cc_final: 0.8872 (tpt) REVERT: b 615 MET cc_start: 0.9029 (pmm) cc_final: 0.8646 (pmm) REVERT: b 834 ASN cc_start: 0.8756 (p0) cc_final: 0.8482 (p0) REVERT: b 837 ASP cc_start: 0.9223 (m-30) cc_final: 0.8936 (m-30) REVERT: b 987 LYS cc_start: 0.8488 (pttt) cc_final: 0.8209 (ptmt) REVERT: b 1013 ASN cc_start: 0.9103 (t0) cc_final: 0.8903 (t0) REVERT: b 1128 LEU cc_start: 0.8933 (mp) cc_final: 0.8647 (mp) REVERT: b 1133 MET cc_start: 0.8776 (mtp) cc_final: 0.8555 (mmm) REVERT: b 1208 MET cc_start: 0.8591 (pmm) cc_final: 0.7676 (pmm) REVERT: c 61 GLU cc_start: 0.9304 (pt0) cc_final: 0.8993 (pm20) REVERT: d 33 PHE cc_start: 0.8631 (m-80) cc_final: 0.8320 (m-10) REVERT: d 70 PHE cc_start: 0.7413 (m-10) cc_final: 0.7115 (m-80) REVERT: e 22 MET cc_start: 0.9485 (tmm) cc_final: 0.9259 (tmm) REVERT: e 60 PHE cc_start: 0.7570 (t80) cc_final: 0.7336 (t80) REVERT: e 114 ASN cc_start: 0.8911 (m-40) cc_final: 0.8263 (m110) REVERT: f 133 VAL cc_start: 0.8151 (m) cc_final: 0.7909 (m) REVERT: g 3 PHE cc_start: 0.8024 (m-10) cc_final: 0.7161 (m-80) REVERT: g 42 PHE cc_start: 0.6474 (m-80) cc_final: 0.6244 (m-80) REVERT: h 123 MET cc_start: 0.6795 (ppp) cc_final: 0.6547 (ppp) REVERT: i 87 GLN cc_start: 0.6183 (pp30) cc_final: 0.5728 (pp30) REVERT: j 1 MET cc_start: 0.7381 (mmm) cc_final: 0.7114 (mmm) REVERT: j 16 ASP cc_start: 0.8724 (p0) cc_final: 0.7632 (t0) REVERT: l 38 LEU cc_start: 0.8174 (mm) cc_final: 0.7849 (mm) outliers start: 2 outliers final: 0 residues processed: 574 average time/residue: 0.4489 time to fit residues: 418.5192 Evaluate side-chains 378 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 20.0000 chunk 302 optimal weight: 40.0000 chunk 167 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 203 optimal weight: 10.0000 chunk 161 optimal weight: 40.0000 chunk 312 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 232 optimal weight: 9.9990 chunk 362 optimal weight: 10.0000 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 390 GLN a 394 ASN a 447 GLN a 742 ASN ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 786 HIS ** a 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1009 ASN ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 ASN ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 158 HIS ** i 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 34167 Z= 0.269 Angle : 0.745 10.714 46545 Z= 0.394 Chirality : 0.046 0.209 5247 Planarity : 0.005 0.051 5704 Dihedral : 16.916 175.919 5419 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 22.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.71 % Favored : 88.27 % Rotamer: Outliers : 1.27 % Allowed : 12.25 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3912 helix: 0.38 (0.14), residues: 1290 sheet: -1.14 (0.21), residues: 575 loop : -2.17 (0.14), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 656 HIS 0.008 0.001 HIS a 451 PHE 0.030 0.002 PHE d 151 TYR 0.021 0.002 TYR b 833 ARG 0.010 0.001 ARG l 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 415 time to evaluate : 3.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 MET cc_start: 0.8156 (tpt) cc_final: 0.7880 (tpt) REVERT: a 108 MET cc_start: 0.8644 (pmm) cc_final: 0.8299 (pmm) REVERT: a 225 ASN cc_start: 0.8808 (t0) cc_final: 0.8354 (t0) REVERT: a 229 SER cc_start: 0.9373 (t) cc_final: 0.8912 (p) REVERT: a 260 ASP cc_start: 0.8315 (m-30) cc_final: 0.8012 (m-30) REVERT: a 266 LEU cc_start: 0.9523 (mt) cc_final: 0.9211 (tt) REVERT: a 444 PHE cc_start: 0.8228 (t80) cc_final: 0.7676 (t80) REVERT: a 455 MET cc_start: 0.7716 (pmm) cc_final: 0.7217 (pmm) REVERT: a 456 MET cc_start: 0.8560 (mpp) cc_final: 0.7654 (mpp) REVERT: a 495 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8602 (mm-30) REVERT: a 515 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8569 (tm-30) REVERT: a 521 MET cc_start: 0.9053 (tpp) cc_final: 0.8113 (mmm) REVERT: a 737 LEU cc_start: 0.7897 (tp) cc_final: 0.7674 (tp) REVERT: a 748 MET cc_start: 0.8662 (mtt) cc_final: 0.8300 (mtt) REVERT: a 760 GLN cc_start: 0.8994 (mt0) cc_final: 0.8726 (mt0) REVERT: a 826 ASP cc_start: 0.8853 (t70) cc_final: 0.8613 (t70) REVERT: a 994 GLN cc_start: 0.8141 (pt0) cc_final: 0.7801 (tt0) REVERT: a 1074 GLU cc_start: 0.8166 (tt0) cc_final: 0.7650 (tt0) REVERT: a 1317 MET cc_start: 0.8691 (tmm) cc_final: 0.8063 (tmm) REVERT: a 1421 CYS cc_start: 0.7920 (t) cc_final: 0.7580 (m) REVERT: a 1426 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8816 (mm-30) REVERT: b 181 LEU cc_start: 0.9166 (mt) cc_final: 0.8769 (tt) REVERT: b 310 MET cc_start: 0.9202 (pmm) cc_final: 0.8920 (pmm) REVERT: b 412 LEU cc_start: 0.9171 (mt) cc_final: 0.8787 (mt) REVERT: b 542 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8729 (mtt) REVERT: b 615 MET cc_start: 0.8895 (pmm) cc_final: 0.8380 (pmm) REVERT: b 809 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7859 (pmm) REVERT: b 834 ASN cc_start: 0.8584 (p0) cc_final: 0.8297 (p0) REVERT: b 837 ASP cc_start: 0.9225 (m-30) cc_final: 0.8980 (m-30) REVERT: b 1013 ASN cc_start: 0.9043 (t0) cc_final: 0.8758 (t0) REVERT: b 1128 LEU cc_start: 0.9027 (mp) cc_final: 0.8803 (mp) REVERT: b 1208 MET cc_start: 0.8647 (pmm) cc_final: 0.7457 (pmm) REVERT: b 1210 MET cc_start: 0.8751 (mmm) cc_final: 0.8190 (mmm) REVERT: c 169 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8762 (ptpt) REVERT: d 33 PHE cc_start: 0.8545 (m-80) cc_final: 0.8339 (m-80) REVERT: e 60 PHE cc_start: 0.7553 (t80) cc_final: 0.7319 (t80) REVERT: e 93 MET cc_start: 0.9385 (ppp) cc_final: 0.9178 (ppp) REVERT: e 114 ASN cc_start: 0.8989 (m-40) cc_final: 0.8335 (m110) REVERT: f 108 PHE cc_start: 0.3903 (m-80) cc_final: 0.3536 (m-80) REVERT: g 106 MET cc_start: 0.3792 (pmm) cc_final: 0.3365 (pmm) REVERT: h 123 MET cc_start: 0.7157 (ppp) cc_final: 0.6653 (ppp) REVERT: j 16 ASP cc_start: 0.8670 (p0) cc_final: 0.7470 (t0) REVERT: k 10 PHE cc_start: 0.7258 (t80) cc_final: 0.7054 (t80) outliers start: 44 outliers final: 26 residues processed: 437 average time/residue: 0.4357 time to fit residues: 319.8036 Evaluate side-chains 379 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 350 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 64 ASN Chi-restraints excluded: chain a residue 86 LEU Chi-restraints excluded: chain a residue 394 ASN Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 1306 LEU Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 179 CYS Chi-restraints excluded: chain b residue 413 LEU Chi-restraints excluded: chain b residue 539 LEU Chi-restraints excluded: chain b residue 542 MET Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 882 THR Chi-restraints excluded: chain b residue 1196 ILE Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain c residue 169 LYS Chi-restraints excluded: chain e residue 21 GLU Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 90 THR Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 72 ASP Chi-restraints excluded: chain i residue 77 LYS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain j residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 201 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 301 optimal weight: 0.9980 chunk 246 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 362 optimal weight: 8.9990 chunk 392 optimal weight: 8.9990 chunk 323 optimal weight: 1.9990 chunk 359 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 291 optimal weight: 50.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 209 ASN a 313 GLN ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 158 HIS ** h 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 34167 Z= 0.226 Angle : 0.702 11.722 46545 Z= 0.367 Chirality : 0.044 0.217 5247 Planarity : 0.004 0.049 5704 Dihedral : 16.823 177.916 5419 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 2.10 % Allowed : 16.96 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3912 helix: 0.58 (0.15), residues: 1290 sheet: -1.06 (0.22), residues: 570 loop : -2.08 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 185 HIS 0.008 0.001 HIS g 158 PHE 0.062 0.002 PHE d 151 TYR 0.019 0.001 TYR b 833 ARG 0.007 0.000 ARG c 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 384 time to evaluate : 3.624 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: a 95 PHE cc_start: 0.8192 (m-10) cc_final: 0.7805 (m-10) REVERT: a 108 MET cc_start: 0.8686 (pmm) cc_final: 0.8294 (pmm) REVERT: a 225 ASN cc_start: 0.8795 (t0) cc_final: 0.8331 (t0) REVERT: a 229 SER cc_start: 0.9414 (t) cc_final: 0.8940 (p) REVERT: a 234 MET cc_start: 0.9201 (tpt) cc_final: 0.8314 (ttt) REVERT: a 260 ASP cc_start: 0.8252 (m-30) cc_final: 0.7978 (m-30) REVERT: a 444 PHE cc_start: 0.8155 (t80) cc_final: 0.7390 (t80) REVERT: a 455 MET cc_start: 0.7888 (pmm) cc_final: 0.7525 (pmm) REVERT: a 456 MET cc_start: 0.8448 (mpp) cc_final: 0.8018 (mpp) REVERT: a 495 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8537 (mm-30) REVERT: a 512 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8376 (p) REVERT: a 515 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8693 (tm-30) REVERT: a 521 MET cc_start: 0.9018 (tpp) cc_final: 0.8247 (mmm) REVERT: a 605 MET cc_start: 0.6002 (tpp) cc_final: 0.5680 (mmt) REVERT: a 748 MET cc_start: 0.8495 (mtt) cc_final: 0.8134 (mtt) REVERT: a 760 GLN cc_start: 0.9012 (mt0) cc_final: 0.8776 (mt0) REVERT: a 826 ASP cc_start: 0.8821 (t70) cc_final: 0.8598 (t70) REVERT: a 994 GLN cc_start: 0.8195 (pt0) cc_final: 0.7887 (tt0) REVERT: a 1074 GLU cc_start: 0.8062 (tt0) cc_final: 0.7236 (tt0) REVERT: a 1317 MET cc_start: 0.8707 (tmm) cc_final: 0.8233 (tmm) REVERT: a 1375 MET cc_start: 0.9199 (tmm) cc_final: 0.8880 (tmm) REVERT: a 1403 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6665 (mm-30) REVERT: a 1421 CYS cc_start: 0.7968 (t) cc_final: 0.7607 (m) REVERT: a 1426 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8771 (mm-30) REVERT: b 181 LEU cc_start: 0.9107 (mt) cc_final: 0.8684 (tt) REVERT: b 412 LEU cc_start: 0.9159 (mt) cc_final: 0.8808 (mt) REVERT: b 542 MET cc_start: 0.8942 (mtp) cc_final: 0.8063 (mtt) REVERT: b 615 MET cc_start: 0.8804 (pmm) cc_final: 0.8388 (pmm) REVERT: b 684 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8854 (tt) REVERT: b 747 MET cc_start: 0.8944 (mmp) cc_final: 0.7980 (mmp) REVERT: b 809 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7983 (pmm) REVERT: b 834 ASN cc_start: 0.8574 (p0) cc_final: 0.8279 (p0) REVERT: b 1013 ASN cc_start: 0.8893 (t0) cc_final: 0.8687 (t0) REVERT: b 1128 LEU cc_start: 0.9032 (mp) cc_final: 0.8798 (mp) REVERT: b 1208 MET cc_start: 0.8681 (pmm) cc_final: 0.7647 (pmm) REVERT: b 1210 MET cc_start: 0.8809 (mmm) cc_final: 0.8164 (mmm) REVERT: c 58 LEU cc_start: 0.8916 (mt) cc_final: 0.8184 (tp) REVERT: c 61 GLU cc_start: 0.9309 (pt0) cc_final: 0.8791 (pm20) REVERT: d 33 PHE cc_start: 0.8574 (m-80) cc_final: 0.8273 (m-80) REVERT: d 151 PHE cc_start: 0.6249 (m-80) cc_final: 0.5977 (m-80) REVERT: e 114 ASN cc_start: 0.9042 (m-40) cc_final: 0.8390 (m110) REVERT: f 103 MET cc_start: 0.8512 (tmm) cc_final: 0.8079 (tmm) REVERT: h 123 MET cc_start: 0.7232 (ppp) cc_final: 0.6716 (ppp) REVERT: j 16 ASP cc_start: 0.8697 (p0) cc_final: 0.7486 (t0) REVERT: l 67 PHE cc_start: 0.9200 (m-10) cc_final: 0.8971 (m-10) outliers start: 73 outliers final: 35 residues processed: 433 average time/residue: 0.4130 time to fit residues: 302.1948 Evaluate side-chains 392 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 354 time to evaluate : 3.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 64 ASN Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 351 THR Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 1337 GLU Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 179 CYS Chi-restraints excluded: chain b residue 413 LEU Chi-restraints excluded: chain b residue 650 GLU Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 1147 LEU Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1166 CYS Chi-restraints excluded: chain b residue 1196 ILE Chi-restraints excluded: chain b residue 1202 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1206 GLU Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain e residue 21 GLU Chi-restraints excluded: chain e residue 150 VAL Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 55 ASP Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 77 LYS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain j residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 358 optimal weight: 8.9990 chunk 272 optimal weight: 0.5980 chunk 188 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 364 optimal weight: 6.9990 chunk 385 optimal weight: 2.9990 chunk 190 optimal weight: 9.9990 chunk 345 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 209 ASN a 313 GLN ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 394 ASN ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 821 GLN ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b1195 HIS ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 158 HIS ** h 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 34167 Z= 0.238 Angle : 0.697 11.333 46545 Z= 0.362 Chirality : 0.044 0.220 5247 Planarity : 0.004 0.056 5704 Dihedral : 16.789 178.071 5419 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 2.57 % Allowed : 18.60 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3912 helix: 0.62 (0.15), residues: 1298 sheet: -1.09 (0.22), residues: 565 loop : -2.03 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 31 HIS 0.008 0.001 HIS g 158 PHE 0.045 0.002 PHE h 118 TYR 0.019 0.001 TYR b 833 ARG 0.007 0.000 ARG b 807 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 366 time to evaluate : 3.745 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: a 41 MET cc_start: 0.7996 (tpt) cc_final: 0.7701 (tpt) REVERT: a 74 MET cc_start: 0.8668 (ttm) cc_final: 0.8448 (ttm) REVERT: a 95 PHE cc_start: 0.8255 (m-10) cc_final: 0.7900 (m-10) REVERT: a 108 MET cc_start: 0.8694 (pmm) cc_final: 0.8274 (pmm) REVERT: a 229 SER cc_start: 0.9433 (t) cc_final: 0.8912 (p) REVERT: a 234 MET cc_start: 0.9211 (tpt) cc_final: 0.8467 (ttt) REVERT: a 260 ASP cc_start: 0.8201 (m-30) cc_final: 0.7934 (m-30) REVERT: a 444 PHE cc_start: 0.8330 (t80) cc_final: 0.7701 (t80) REVERT: a 455 MET cc_start: 0.7861 (pmm) cc_final: 0.7469 (pmm) REVERT: a 456 MET cc_start: 0.8469 (mpp) cc_final: 0.8000 (mpp) REVERT: a 495 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8555 (mm-30) REVERT: a 515 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8686 (tm-30) REVERT: a 605 MET cc_start: 0.6273 (tpp) cc_final: 0.5680 (mmt) REVERT: a 737 LEU cc_start: 0.7855 (tp) cc_final: 0.7578 (tp) REVERT: a 760 GLN cc_start: 0.9014 (mt0) cc_final: 0.8758 (mt0) REVERT: a 826 ASP cc_start: 0.8850 (t70) cc_final: 0.8629 (t70) REVERT: a 994 GLN cc_start: 0.8320 (pt0) cc_final: 0.8023 (tt0) REVERT: a 1317 MET cc_start: 0.8657 (tmm) cc_final: 0.8124 (tmm) REVERT: a 1375 MET cc_start: 0.9184 (tmm) cc_final: 0.8852 (tmm) REVERT: a 1403 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6682 (mm-30) REVERT: a 1421 CYS cc_start: 0.7971 (t) cc_final: 0.7587 (m) REVERT: a 1426 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8661 (mm-30) REVERT: b 181 LEU cc_start: 0.9105 (mt) cc_final: 0.8536 (tt) REVERT: b 412 LEU cc_start: 0.9169 (mt) cc_final: 0.8826 (mt) REVERT: b 542 MET cc_start: 0.8918 (mtp) cc_final: 0.7934 (mtt) REVERT: b 747 MET cc_start: 0.8938 (mmp) cc_final: 0.7919 (mmp) REVERT: b 834 ASN cc_start: 0.8522 (p0) cc_final: 0.8217 (p0) REVERT: b 1021 MET cc_start: 0.7985 (mmt) cc_final: 0.7664 (mmt) REVERT: b 1111 MET cc_start: 0.8955 (tpp) cc_final: 0.8718 (tpp) REVERT: b 1128 LEU cc_start: 0.9049 (mp) cc_final: 0.8798 (mp) REVERT: b 1208 MET cc_start: 0.8751 (pmm) cc_final: 0.7779 (pmm) REVERT: c 58 LEU cc_start: 0.8874 (mt) cc_final: 0.8147 (tp) REVERT: e 60 PHE cc_start: 0.6977 (t80) cc_final: 0.6637 (t80) REVERT: e 93 MET cc_start: 0.9330 (ppp) cc_final: 0.9030 (ppp) REVERT: e 114 ASN cc_start: 0.9067 (m-40) cc_final: 0.8422 (m110) REVERT: e 121 MET cc_start: 0.9621 (tpp) cc_final: 0.9395 (tpp) REVERT: f 103 MET cc_start: 0.8390 (tmm) cc_final: 0.8026 (tmm) REVERT: h 97 MET cc_start: 0.8150 (tmm) cc_final: 0.7923 (ppp) REVERT: h 123 MET cc_start: 0.7132 (ppp) cc_final: 0.6767 (ppp) REVERT: i 48 LEU cc_start: 0.9058 (tt) cc_final: 0.8843 (pp) REVERT: j 16 ASP cc_start: 0.8722 (p0) cc_final: 0.7505 (t0) REVERT: k 1 MET cc_start: 0.9475 (tpp) cc_final: 0.9071 (tpp) outliers start: 89 outliers final: 49 residues processed: 430 average time/residue: 0.4158 time to fit residues: 302.1203 Evaluate side-chains 386 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 337 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 64 ASN Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 202 LEU Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 351 THR Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 507 VAL Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 856 THR Chi-restraints excluded: chain a residue 1019 CYS Chi-restraints excluded: chain a residue 1337 GLU Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1394 THR Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 179 CYS Chi-restraints excluded: chain b residue 413 LEU Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 1147 LEU Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1166 CYS Chi-restraints excluded: chain b residue 1196 ILE Chi-restraints excluded: chain b residue 1202 LEU Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain e residue 21 GLU Chi-restraints excluded: chain e residue 74 ASP Chi-restraints excluded: chain e residue 150 VAL Chi-restraints excluded: chain e residue 202 SER Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 115 THR Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 ASP Chi-restraints excluded: chain g residue 158 HIS Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 77 LYS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain j residue 52 THR Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain l residue 44 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 321 optimal weight: 0.1980 chunk 218 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 329 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 196 optimal weight: 7.9990 chunk 346 optimal weight: 7.9990 chunk 97 optimal weight: 0.1980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 124 GLN a 209 ASN a 299 HIS a 313 GLN a 390 GLN ** a 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 877 HIS ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 73 GLN ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 587 HIS ** b 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 203 GLN ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 113 GLN e 153 HIS g 158 HIS h 35 GLN ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 34167 Z= 0.183 Angle : 0.691 10.384 46545 Z= 0.354 Chirality : 0.044 0.234 5247 Planarity : 0.004 0.053 5704 Dihedral : 16.708 178.518 5419 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 2.28 % Allowed : 20.30 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3912 helix: 0.71 (0.15), residues: 1300 sheet: -0.92 (0.22), residues: 544 loop : -1.98 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 185 HIS 0.018 0.001 HIS a 299 PHE 0.063 0.001 PHE d 151 TYR 0.015 0.001 TYR b 833 ARG 0.019 0.000 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 384 time to evaluate : 4.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 95 PHE cc_start: 0.8128 (m-10) cc_final: 0.7803 (m-10) REVERT: a 108 MET cc_start: 0.8786 (pmm) cc_final: 0.8362 (pmm) REVERT: a 229 SER cc_start: 0.9384 (t) cc_final: 0.8865 (p) REVERT: a 234 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8566 (ttt) REVERT: a 260 ASP cc_start: 0.7964 (m-30) cc_final: 0.7719 (m-30) REVERT: a 261 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7005 (t0) REVERT: a 304 MET cc_start: 0.9274 (tpt) cc_final: 0.8856 (tpt) REVERT: a 444 PHE cc_start: 0.8267 (t80) cc_final: 0.7542 (t80) REVERT: a 455 MET cc_start: 0.7600 (pmm) cc_final: 0.7287 (pmm) REVERT: a 456 MET cc_start: 0.8446 (mpp) cc_final: 0.8115 (mpp) REVERT: a 474 VAL cc_start: 0.9624 (t) cc_final: 0.9277 (p) REVERT: a 495 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8463 (mm-30) REVERT: a 507 VAL cc_start: 0.9500 (p) cc_final: 0.9273 (m) REVERT: a 515 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8538 (tm-30) REVERT: a 521 MET cc_start: 0.8875 (mmm) cc_final: 0.8121 (mmm) REVERT: a 547 LEU cc_start: 0.8171 (mt) cc_final: 0.7883 (mt) REVERT: a 605 MET cc_start: 0.6473 (tpp) cc_final: 0.5882 (mmt) REVERT: a 748 MET cc_start: 0.8786 (mtt) cc_final: 0.8321 (mtt) REVERT: a 760 GLN cc_start: 0.9003 (mt0) cc_final: 0.8781 (mt0) REVERT: a 826 ASP cc_start: 0.8786 (t70) cc_final: 0.8578 (t70) REVERT: a 994 GLN cc_start: 0.8360 (pt0) cc_final: 0.8072 (tt0) REVERT: a 1013 ASP cc_start: 0.7828 (m-30) cc_final: 0.7600 (p0) REVERT: a 1317 MET cc_start: 0.8582 (tmm) cc_final: 0.8251 (tmm) REVERT: a 1375 MET cc_start: 0.9137 (tmm) cc_final: 0.8860 (tmm) REVERT: a 1403 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6862 (mm-30) REVERT: a 1421 CYS cc_start: 0.7972 (t) cc_final: 0.7587 (m) REVERT: a 1426 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8751 (mm-30) REVERT: b 181 LEU cc_start: 0.9041 (mt) cc_final: 0.8482 (tt) REVERT: b 391 ASP cc_start: 0.9450 (m-30) cc_final: 0.8748 (t0) REVERT: b 412 LEU cc_start: 0.9156 (mt) cc_final: 0.8833 (mt) REVERT: b 521 LEU cc_start: 0.9290 (tp) cc_final: 0.9023 (mm) REVERT: b 542 MET cc_start: 0.8876 (mtp) cc_final: 0.7674 (mtt) REVERT: b 597 MET cc_start: 0.9385 (ttp) cc_final: 0.8903 (tmm) REVERT: b 616 ILE cc_start: 0.7779 (pt) cc_final: 0.7409 (pt) REVERT: b 747 MET cc_start: 0.8844 (mmp) cc_final: 0.7780 (mmp) REVERT: b 834 ASN cc_start: 0.8442 (p0) cc_final: 0.7779 (p0) REVERT: b 1021 MET cc_start: 0.7945 (mmt) cc_final: 0.7596 (mmp) REVERT: b 1111 MET cc_start: 0.8957 (tpp) cc_final: 0.8669 (tpp) REVERT: b 1208 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7705 (pmm) REVERT: b 1210 MET cc_start: 0.8886 (mmm) cc_final: 0.8277 (mmm) REVERT: c 58 LEU cc_start: 0.8855 (mt) cc_final: 0.8121 (tp) REVERT: e 60 PHE cc_start: 0.6931 (t80) cc_final: 0.6651 (t80) REVERT: e 93 MET cc_start: 0.9262 (ppp) cc_final: 0.8997 (ppp) REVERT: e 114 ASN cc_start: 0.9084 (m-40) cc_final: 0.8401 (m110) REVERT: e 121 MET cc_start: 0.9638 (tpp) cc_final: 0.9371 (tpp) REVERT: f 103 MET cc_start: 0.8393 (tmm) cc_final: 0.8171 (tmm) REVERT: h 89 LEU cc_start: 0.9368 (tt) cc_final: 0.8983 (pt) REVERT: h 97 MET cc_start: 0.8378 (tmm) cc_final: 0.8128 (tmm) REVERT: h 123 MET cc_start: 0.7148 (ppp) cc_final: 0.6767 (ppp) REVERT: j 16 ASP cc_start: 0.8666 (p0) cc_final: 0.7358 (t0) REVERT: j 19 GLU cc_start: 0.8100 (mp0) cc_final: 0.7821 (mp0) REVERT: j 58 GLU cc_start: 0.9458 (mm-30) cc_final: 0.8830 (mp0) REVERT: k 1 MET cc_start: 0.9536 (tpp) cc_final: 0.9335 (tpp) REVERT: l 67 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8656 (m-10) outliers start: 79 outliers final: 44 residues processed: 444 average time/residue: 0.4146 time to fit residues: 312.9350 Evaluate side-chains 391 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 343 time to evaluate : 3.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 64 ASN Chi-restraints excluded: chain a residue 124 GLN Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 234 MET Chi-restraints excluded: chain a residue 261 ASP Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 856 THR Chi-restraints excluded: chain a residue 1019 CYS Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 286 PHE Chi-restraints excluded: chain b residue 603 LEU Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 694 ASP Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 1023 VAL Chi-restraints excluded: chain b residue 1147 LEU Chi-restraints excluded: chain b residue 1156 ASP Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1166 CYS Chi-restraints excluded: chain b residue 1196 ILE Chi-restraints excluded: chain b residue 1202 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 27 LEU Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain e residue 150 VAL Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 115 THR Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 ASP Chi-restraints excluded: chain g residue 163 ILE Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain l residue 67 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 129 optimal weight: 40.0000 chunk 347 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 226 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 386 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 209 ASN a 313 GLN ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 390 GLN a 394 ASN a 447 GLN a 659 HIS ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN g 158 HIS ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 34167 Z= 0.359 Angle : 0.753 9.895 46545 Z= 0.395 Chirality : 0.045 0.232 5247 Planarity : 0.005 0.071 5704 Dihedral : 16.835 178.047 5419 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 24.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 3.29 % Allowed : 21.11 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3912 helix: 0.62 (0.15), residues: 1298 sheet: -1.17 (0.21), residues: 592 loop : -2.12 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP b 31 HIS 0.011 0.002 HIS b 363 PHE 0.060 0.002 PHE d 151 TYR 0.023 0.002 TYR b 833 ARG 0.007 0.001 ARG c 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 343 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 95 PHE cc_start: 0.8297 (m-10) cc_final: 0.7971 (m-10) REVERT: a 108 MET cc_start: 0.8765 (pmm) cc_final: 0.8362 (pmm) REVERT: a 229 SER cc_start: 0.9376 (t) cc_final: 0.8880 (p) REVERT: a 234 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8588 (ttt) REVERT: a 260 ASP cc_start: 0.7996 (m-30) cc_final: 0.7742 (m-30) REVERT: a 261 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7179 (t0) REVERT: a 304 MET cc_start: 0.9396 (tpt) cc_final: 0.8971 (tpt) REVERT: a 455 MET cc_start: 0.7665 (pmm) cc_final: 0.6963 (pmm) REVERT: a 456 MET cc_start: 0.8663 (mpp) cc_final: 0.7393 (mpp) REVERT: a 474 VAL cc_start: 0.9660 (t) cc_final: 0.9297 (p) REVERT: a 507 VAL cc_start: 0.9481 (OUTLIER) cc_final: 0.9239 (m) REVERT: a 515 GLN cc_start: 0.9263 (tm-30) cc_final: 0.8681 (tm-30) REVERT: a 521 MET cc_start: 0.9096 (mmm) cc_final: 0.8404 (mmm) REVERT: a 605 MET cc_start: 0.6620 (tpp) cc_final: 0.6060 (mmt) REVERT: a 708 MET cc_start: 0.7079 (pmm) cc_final: 0.6791 (pmm) REVERT: a 760 GLN cc_start: 0.9014 (mt0) cc_final: 0.8808 (mt0) REVERT: a 826 ASP cc_start: 0.8939 (t70) cc_final: 0.8704 (t70) REVERT: a 994 GLN cc_start: 0.8302 (pt0) cc_final: 0.7853 (tt0) REVERT: a 1074 GLU cc_start: 0.8103 (tt0) cc_final: 0.7363 (tt0) REVERT: a 1116 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8327 (pp) REVERT: a 1317 MET cc_start: 0.8700 (tmm) cc_final: 0.8388 (tmm) REVERT: a 1375 MET cc_start: 0.9189 (tmm) cc_final: 0.8771 (tmm) REVERT: a 1400 CYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8669 (p) REVERT: a 1421 CYS cc_start: 0.8066 (t) cc_final: 0.7405 (m) REVERT: a 1426 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8725 (mm-30) REVERT: a 1427 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8738 (t0) REVERT: b 391 ASP cc_start: 0.9437 (m-30) cc_final: 0.8828 (t0) REVERT: b 412 LEU cc_start: 0.9200 (mt) cc_final: 0.8877 (mt) REVERT: b 542 MET cc_start: 0.8979 (mtp) cc_final: 0.8652 (mtt) REVERT: b 597 MET cc_start: 0.9446 (ttp) cc_final: 0.9005 (tmm) REVERT: b 616 ILE cc_start: 0.7907 (pt) cc_final: 0.7672 (mp) REVERT: b 834 ASN cc_start: 0.8313 (p0) cc_final: 0.8004 (p0) REVERT: b 1111 MET cc_start: 0.8924 (tpp) cc_final: 0.8596 (tpp) REVERT: b 1201 LYS cc_start: 0.9273 (pptt) cc_final: 0.8963 (ttpp) REVERT: b 1208 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8011 (pmm) REVERT: b 1210 MET cc_start: 0.8944 (mmm) cc_final: 0.8444 (mmm) REVERT: c 58 LEU cc_start: 0.8732 (mt) cc_final: 0.7998 (tp) REVERT: e 93 MET cc_start: 0.9308 (ppp) cc_final: 0.9065 (ppp) REVERT: e 114 ASN cc_start: 0.9079 (m-40) cc_final: 0.8437 (p0) REVERT: f 103 MET cc_start: 0.8460 (tmm) cc_final: 0.8159 (tmm) REVERT: h 89 LEU cc_start: 0.9335 (tt) cc_final: 0.8921 (pt) REVERT: h 97 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8481 (tmm) REVERT: h 116 TYR cc_start: 0.7442 (m-80) cc_final: 0.7199 (m-80) REVERT: h 123 MET cc_start: 0.7304 (ppp) cc_final: 0.6979 (ppp) REVERT: j 16 ASP cc_start: 0.8791 (p0) cc_final: 0.7254 (t0) REVERT: l 67 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8553 (m-10) outliers start: 114 outliers final: 73 residues processed: 424 average time/residue: 0.3991 time to fit residues: 291.1738 Evaluate side-chains 412 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 330 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 64 ASN Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 202 LEU Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 234 MET Chi-restraints excluded: chain a residue 261 ASP Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 351 THR Chi-restraints excluded: chain a residue 394 ASN Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 507 VAL Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 650 GLN Chi-restraints excluded: chain a residue 762 SER Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 856 THR Chi-restraints excluded: chain a residue 863 VAL Chi-restraints excluded: chain a residue 1019 CYS Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1116 LEU Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1232 ASN Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1394 THR Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain a residue 1427 ASN Chi-restraints excluded: chain b residue 413 LEU Chi-restraints excluded: chain b residue 650 GLU Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 694 ASP Chi-restraints excluded: chain b residue 748 ILE Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 1023 VAL Chi-restraints excluded: chain b residue 1099 VAL Chi-restraints excluded: chain b residue 1147 LEU Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1166 CYS Chi-restraints excluded: chain b residue 1196 ILE Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain c residue 163 ILE Chi-restraints excluded: chain c residue 238 ILE Chi-restraints excluded: chain c residue 243 VAL Chi-restraints excluded: chain e residue 21 GLU Chi-restraints excluded: chain e residue 74 ASP Chi-restraints excluded: chain e residue 178 ILE Chi-restraints excluded: chain e residue 202 SER Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 133 VAL Chi-restraints excluded: chain f residue 151 LEU Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 ASP Chi-restraints excluded: chain g residue 158 HIS Chi-restraints excluded: chain g residue 163 ILE Chi-restraints excluded: chain h residue 97 MET Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain j residue 52 THR Chi-restraints excluded: chain j residue 61 LEU Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain l residue 31 CYS Chi-restraints excluded: chain l residue 44 ASP Chi-restraints excluded: chain l residue 67 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 372 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 281 optimal weight: 6.9990 chunk 218 optimal weight: 0.0970 chunk 324 optimal weight: 7.9990 chunk 215 optimal weight: 0.5980 chunk 384 optimal weight: 20.0000 chunk 240 optimal weight: 7.9990 chunk 234 optimal weight: 30.0000 chunk 177 optimal weight: 8.9990 overall best weight: 2.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 390 GLN a 659 HIS ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34167 Z= 0.192 Angle : 0.707 10.870 46545 Z= 0.361 Chirality : 0.044 0.231 5247 Planarity : 0.004 0.049 5704 Dihedral : 16.756 178.565 5419 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 2.85 % Allowed : 21.60 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.14), residues: 3912 helix: 0.78 (0.15), residues: 1304 sheet: -1.00 (0.22), residues: 570 loop : -2.06 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 185 HIS 0.033 0.001 HIS g 158 PHE 0.056 0.001 PHE d 151 TYR 0.016 0.001 TYR b 833 ARG 0.009 0.000 ARG k 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 366 time to evaluate : 4.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 95 PHE cc_start: 0.8194 (m-10) cc_final: 0.7832 (m-10) REVERT: a 108 MET cc_start: 0.8802 (pmm) cc_final: 0.8375 (pmm) REVERT: a 122 MET cc_start: 0.9099 (pmm) cc_final: 0.8841 (pmm) REVERT: a 229 SER cc_start: 0.9357 (t) cc_final: 0.8836 (p) REVERT: a 234 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8625 (ttt) REVERT: a 260 ASP cc_start: 0.7703 (m-30) cc_final: 0.7473 (m-30) REVERT: a 261 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7106 (t0) REVERT: a 394 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8220 (t0) REVERT: a 444 PHE cc_start: 0.8301 (t80) cc_final: 0.7618 (t80) REVERT: a 455 MET cc_start: 0.7524 (pmm) cc_final: 0.7211 (pmm) REVERT: a 456 MET cc_start: 0.8539 (mpp) cc_final: 0.8189 (mpp) REVERT: a 474 VAL cc_start: 0.9608 (t) cc_final: 0.9232 (p) REVERT: a 507 VAL cc_start: 0.9496 (OUTLIER) cc_final: 0.9252 (m) REVERT: a 515 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8590 (tm-30) REVERT: a 521 MET cc_start: 0.8994 (mmm) cc_final: 0.8228 (mmm) REVERT: a 605 MET cc_start: 0.6756 (tpp) cc_final: 0.6421 (tpp) REVERT: a 708 MET cc_start: 0.7191 (pmm) cc_final: 0.6906 (pmm) REVERT: a 760 GLN cc_start: 0.9054 (mt0) cc_final: 0.8853 (mt0) REVERT: a 818 MET cc_start: 0.9575 (mmt) cc_final: 0.9197 (mmp) REVERT: a 826 ASP cc_start: 0.8764 (t70) cc_final: 0.8556 (t70) REVERT: a 864 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.8940 (tp) REVERT: a 994 GLN cc_start: 0.8330 (pt0) cc_final: 0.7842 (tt0) REVERT: a 1074 GLU cc_start: 0.7913 (tt0) cc_final: 0.7226 (tt0) REVERT: a 1116 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8220 (pp) REVERT: a 1317 MET cc_start: 0.8652 (tmm) cc_final: 0.8312 (tmm) REVERT: a 1375 MET cc_start: 0.9146 (tmm) cc_final: 0.8811 (tmm) REVERT: a 1400 CYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8626 (p) REVERT: a 1403 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6799 (mm-30) REVERT: a 1421 CYS cc_start: 0.8096 (t) cc_final: 0.7603 (m) REVERT: a 1426 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8600 (mm-30) REVERT: b 181 LEU cc_start: 0.8988 (mp) cc_final: 0.8343 (tt) REVERT: b 239 GLU cc_start: 0.8878 (tp30) cc_final: 0.8434 (tm-30) REVERT: b 385 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9235 (tp) REVERT: b 391 ASP cc_start: 0.9447 (m-30) cc_final: 0.8748 (t0) REVERT: b 412 LEU cc_start: 0.9148 (mt) cc_final: 0.8831 (mt) REVERT: b 521 LEU cc_start: 0.9285 (tp) cc_final: 0.9034 (mm) REVERT: b 542 MET cc_start: 0.8872 (mtp) cc_final: 0.7471 (mtt) REVERT: b 705 MET cc_start: 0.6808 (tmm) cc_final: 0.6579 (tpp) REVERT: b 747 MET cc_start: 0.8742 (mmp) cc_final: 0.7709 (mmp) REVERT: b 834 ASN cc_start: 0.8227 (p0) cc_final: 0.7759 (m-40) REVERT: b 931 TYR cc_start: 0.7891 (m-80) cc_final: 0.7527 (t80) REVERT: b 1021 MET cc_start: 0.8020 (mmt) cc_final: 0.7725 (mmt) REVERT: b 1111 MET cc_start: 0.8904 (tpp) cc_final: 0.8568 (tpp) REVERT: b 1208 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.7709 (pmm) REVERT: c 58 LEU cc_start: 0.8733 (mt) cc_final: 0.7987 (tp) REVERT: e 93 MET cc_start: 0.9272 (ppp) cc_final: 0.9023 (ppp) REVERT: e 114 ASN cc_start: 0.9065 (m-40) cc_final: 0.8448 (m110) REVERT: f 103 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8154 (tmm) REVERT: h 89 LEU cc_start: 0.9322 (tt) cc_final: 0.8927 (pt) REVERT: h 116 TYR cc_start: 0.7381 (m-80) cc_final: 0.7179 (m-80) REVERT: h 123 MET cc_start: 0.7628 (ppp) cc_final: 0.7372 (ppp) REVERT: j 16 ASP cc_start: 0.8686 (p0) cc_final: 0.7256 (t0) REVERT: j 58 GLU cc_start: 0.9447 (mm-30) cc_final: 0.8817 (mp0) REVERT: k 1 MET cc_start: 0.9519 (tpp) cc_final: 0.9292 (tpp) REVERT: l 67 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8518 (m-10) outliers start: 99 outliers final: 63 residues processed: 443 average time/residue: 0.4040 time to fit residues: 306.8339 Evaluate side-chains 417 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 343 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 64 ASN Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 234 MET Chi-restraints excluded: chain a residue 261 ASP Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 351 THR Chi-restraints excluded: chain a residue 394 ASN Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 507 VAL Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 650 GLN Chi-restraints excluded: chain a residue 658 LEU Chi-restraints excluded: chain a residue 762 SER Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 856 THR Chi-restraints excluded: chain a residue 864 ILE Chi-restraints excluded: chain a residue 965 GLN Chi-restraints excluded: chain a residue 1019 CYS Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1107 VAL Chi-restraints excluded: chain a residue 1116 LEU Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1318 THR Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 385 LEU Chi-restraints excluded: chain b residue 466 TRP Chi-restraints excluded: chain b residue 603 LEU Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 694 ASP Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 870 ILE Chi-restraints excluded: chain b residue 1023 VAL Chi-restraints excluded: chain b residue 1028 GLU Chi-restraints excluded: chain b residue 1147 LEU Chi-restraints excluded: chain b residue 1156 ASP Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1166 CYS Chi-restraints excluded: chain b residue 1196 ILE Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain c residue 238 ILE Chi-restraints excluded: chain e residue 74 ASP Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 103 MET Chi-restraints excluded: chain f residue 133 VAL Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 ASP Chi-restraints excluded: chain g residue 163 ILE Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 77 LYS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain l residue 44 ASP Chi-restraints excluded: chain l residue 67 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 237 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 229 optimal weight: 0.0040 chunk 115 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 262 optimal weight: 0.7980 chunk 190 optimal weight: 9.9990 chunk 35 optimal weight: 0.0670 chunk 302 optimal weight: 9.9990 overall best weight: 2.7734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 390 GLN a 394 ASN a 659 HIS ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 GLN ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 158 HIS ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 34167 Z= 0.207 Angle : 0.709 11.865 46545 Z= 0.361 Chirality : 0.043 0.231 5247 Planarity : 0.004 0.049 5704 Dihedral : 16.711 178.153 5419 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 2.71 % Allowed : 22.20 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3912 helix: 0.77 (0.15), residues: 1305 sheet: -0.93 (0.22), residues: 546 loop : -2.04 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 185 HIS 0.009 0.001 HIS g 158 PHE 0.055 0.001 PHE d 151 TYR 0.019 0.001 TYR b 833 ARG 0.008 0.000 ARG f 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 353 time to evaluate : 3.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 95 PHE cc_start: 0.8295 (m-10) cc_final: 0.7970 (m-10) REVERT: a 108 MET cc_start: 0.8870 (pmm) cc_final: 0.8438 (pmm) REVERT: a 122 MET cc_start: 0.9143 (pmm) cc_final: 0.8908 (pmm) REVERT: a 229 SER cc_start: 0.9353 (t) cc_final: 0.8848 (p) REVERT: a 234 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8568 (ttt) REVERT: a 260 ASP cc_start: 0.7636 (m-30) cc_final: 0.7416 (m-30) REVERT: a 261 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7125 (t0) REVERT: a 455 MET cc_start: 0.7586 (pmm) cc_final: 0.6928 (pmm) REVERT: a 456 MET cc_start: 0.8550 (mpp) cc_final: 0.7684 (mpp) REVERT: a 474 VAL cc_start: 0.9599 (t) cc_final: 0.9226 (p) REVERT: a 507 VAL cc_start: 0.9485 (OUTLIER) cc_final: 0.9249 (m) REVERT: a 515 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8562 (tm-30) REVERT: a 521 MET cc_start: 0.9033 (mmm) cc_final: 0.8252 (mmm) REVERT: a 605 MET cc_start: 0.6767 (tpp) cc_final: 0.6441 (tpp) REVERT: a 708 MET cc_start: 0.6970 (pmm) cc_final: 0.6723 (pmm) REVERT: a 760 GLN cc_start: 0.9097 (mt0) cc_final: 0.8892 (mt0) REVERT: a 826 ASP cc_start: 0.8861 (t70) cc_final: 0.8655 (t70) REVERT: a 864 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.8931 (tp) REVERT: a 994 GLN cc_start: 0.8361 (pt0) cc_final: 0.7892 (tt0) REVERT: a 1074 GLU cc_start: 0.7927 (tt0) cc_final: 0.7243 (tt0) REVERT: a 1116 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8246 (pp) REVERT: a 1317 MET cc_start: 0.8653 (tmm) cc_final: 0.8306 (tmm) REVERT: a 1375 MET cc_start: 0.9139 (tmm) cc_final: 0.8826 (tmm) REVERT: a 1400 CYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8591 (p) REVERT: a 1403 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6768 (mm-30) REVERT: a 1421 CYS cc_start: 0.8029 (t) cc_final: 0.7501 (m) REVERT: a 1426 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8798 (mm-30) REVERT: b 239 GLU cc_start: 0.8824 (tp30) cc_final: 0.8422 (tm-30) REVERT: b 391 ASP cc_start: 0.9437 (m-30) cc_final: 0.8763 (t0) REVERT: b 412 LEU cc_start: 0.9149 (mt) cc_final: 0.8835 (mt) REVERT: b 542 MET cc_start: 0.8868 (mtp) cc_final: 0.7413 (mtt) REVERT: b 747 MET cc_start: 0.8751 (mmp) cc_final: 0.7730 (mmp) REVERT: b 834 ASN cc_start: 0.8235 (p0) cc_final: 0.7856 (m110) REVERT: b 931 TYR cc_start: 0.7997 (m-80) cc_final: 0.7659 (t80) REVERT: b 1021 MET cc_start: 0.7983 (mmt) cc_final: 0.7543 (mmp) REVERT: b 1111 MET cc_start: 0.8886 (tpp) cc_final: 0.8606 (tpp) REVERT: b 1208 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.7693 (pmm) REVERT: c 58 LEU cc_start: 0.8755 (mt) cc_final: 0.7975 (tp) REVERT: e 93 MET cc_start: 0.9276 (ppp) cc_final: 0.9037 (ppp) REVERT: e 114 ASN cc_start: 0.9107 (m-40) cc_final: 0.8322 (p0) REVERT: f 103 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8152 (tmm) REVERT: f 110 ASP cc_start: 0.8678 (p0) cc_final: 0.8402 (p0) REVERT: f 112 GLU cc_start: 0.9321 (mm-30) cc_final: 0.9059 (mp0) REVERT: h 97 MET cc_start: 0.7663 (tmm) cc_final: 0.7218 (tmm) REVERT: h 116 TYR cc_start: 0.7498 (m-80) cc_final: 0.7119 (m-80) REVERT: h 123 MET cc_start: 0.7793 (ppp) cc_final: 0.7436 (ppp) REVERT: j 16 ASP cc_start: 0.8723 (p0) cc_final: 0.7281 (t0) REVERT: j 58 GLU cc_start: 0.9449 (mm-30) cc_final: 0.8803 (mp0) REVERT: k 1 MET cc_start: 0.9541 (tpp) cc_final: 0.9096 (tpp) REVERT: l 67 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8588 (m-10) outliers start: 94 outliers final: 71 residues processed: 426 average time/residue: 0.4093 time to fit residues: 301.6926 Evaluate side-chains 419 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 339 time to evaluate : 3.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 64 ASN Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 234 MET Chi-restraints excluded: chain a residue 261 ASP Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 507 VAL Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 650 GLN Chi-restraints excluded: chain a residue 658 LEU Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 856 THR Chi-restraints excluded: chain a residue 863 VAL Chi-restraints excluded: chain a residue 864 ILE Chi-restraints excluded: chain a residue 965 GLN Chi-restraints excluded: chain a residue 1019 CYS Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1107 VAL Chi-restraints excluded: chain a residue 1116 LEU Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1318 THR Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 466 TRP Chi-restraints excluded: chain b residue 539 LEU Chi-restraints excluded: chain b residue 603 LEU Chi-restraints excluded: chain b residue 651 LEU Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 694 ASP Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 840 ILE Chi-restraints excluded: chain b residue 870 ILE Chi-restraints excluded: chain b residue 1023 VAL Chi-restraints excluded: chain b residue 1028 GLU Chi-restraints excluded: chain b residue 1099 VAL Chi-restraints excluded: chain b residue 1147 LEU Chi-restraints excluded: chain b residue 1156 ASP Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1166 CYS Chi-restraints excluded: chain b residue 1196 ILE Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain c residue 238 ILE Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain e residue 5 ASN Chi-restraints excluded: chain e residue 150 VAL Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 103 MET Chi-restraints excluded: chain f residue 133 VAL Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 ASP Chi-restraints excluded: chain g residue 158 HIS Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 77 LYS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain l residue 31 CYS Chi-restraints excluded: chain l residue 44 ASP Chi-restraints excluded: chain l residue 67 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 349 optimal weight: 30.0000 chunk 368 optimal weight: 20.0000 chunk 336 optimal weight: 20.0000 chunk 358 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 323 optimal weight: 7.9990 chunk 338 optimal weight: 6.9990 chunk 357 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 469 GLN b 763 GLN ** b 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 158 HIS ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34167 Z= 0.282 Angle : 0.744 14.307 46545 Z= 0.380 Chirality : 0.044 0.232 5247 Planarity : 0.004 0.051 5704 Dihedral : 16.782 177.765 5419 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 2.83 % Allowed : 22.17 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3912 helix: 0.76 (0.15), residues: 1305 sheet: -0.96 (0.22), residues: 564 loop : -2.10 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 185 HIS 0.025 0.001 HIS g 158 PHE 0.056 0.002 PHE d 151 TYR 0.021 0.001 TYR b 833 ARG 0.008 0.000 ARG f 119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 336 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 95 PHE cc_start: 0.8311 (m-10) cc_final: 0.7987 (m-10) REVERT: a 108 MET cc_start: 0.8796 (pmm) cc_final: 0.8348 (pmm) REVERT: a 122 MET cc_start: 0.9192 (pmm) cc_final: 0.8974 (pmm) REVERT: a 229 SER cc_start: 0.9359 (t) cc_final: 0.8858 (p) REVERT: a 234 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8570 (ttt) REVERT: a 260 ASP cc_start: 0.7756 (m-30) cc_final: 0.7531 (m-30) REVERT: a 261 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7215 (t0) REVERT: a 304 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8908 (tpp) REVERT: a 455 MET cc_start: 0.7582 (pmm) cc_final: 0.6957 (pmm) REVERT: a 456 MET cc_start: 0.8722 (mpp) cc_final: 0.7750 (mpp) REVERT: a 474 VAL cc_start: 0.9613 (t) cc_final: 0.9238 (p) REVERT: a 515 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8616 (tm-30) REVERT: a 521 MET cc_start: 0.9082 (mmm) cc_final: 0.8334 (mmm) REVERT: a 605 MET cc_start: 0.6913 (tpp) cc_final: 0.6605 (tpp) REVERT: a 708 MET cc_start: 0.6844 (pmm) cc_final: 0.6595 (pmm) REVERT: a 760 GLN cc_start: 0.9084 (mt0) cc_final: 0.8870 (mt0) REVERT: a 826 ASP cc_start: 0.8887 (t70) cc_final: 0.8657 (t70) REVERT: a 864 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.8978 (tp) REVERT: a 994 GLN cc_start: 0.8373 (pt0) cc_final: 0.7756 (tt0) REVERT: a 1116 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8246 (pp) REVERT: a 1317 MET cc_start: 0.8694 (tmm) cc_final: 0.8357 (tmm) REVERT: a 1375 MET cc_start: 0.9156 (tmm) cc_final: 0.8797 (tmm) REVERT: a 1400 CYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8617 (p) REVERT: a 1421 CYS cc_start: 0.8032 (t) cc_final: 0.7594 (p) REVERT: a 1426 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8744 (mm-30) REVERT: b 412 LEU cc_start: 0.9182 (mt) cc_final: 0.8866 (mt) REVERT: b 542 MET cc_start: 0.8898 (mtp) cc_final: 0.7444 (mtt) REVERT: b 747 MET cc_start: 0.8744 (mmp) cc_final: 0.7752 (mmp) REVERT: b 834 ASN cc_start: 0.8287 (p0) cc_final: 0.7875 (m-40) REVERT: b 1021 MET cc_start: 0.8027 (mmt) cc_final: 0.7653 (mmt) REVERT: b 1111 MET cc_start: 0.8807 (tpp) cc_final: 0.8578 (tpp) REVERT: b 1208 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7783 (pmm) REVERT: c 58 LEU cc_start: 0.8756 (mt) cc_final: 0.7971 (tp) REVERT: e 93 MET cc_start: 0.9304 (ppp) cc_final: 0.9068 (ppp) REVERT: e 114 ASN cc_start: 0.9113 (m-40) cc_final: 0.8369 (p0) REVERT: f 103 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8166 (tmm) REVERT: h 116 TYR cc_start: 0.7327 (m-80) cc_final: 0.7011 (m-80) REVERT: h 123 MET cc_start: 0.7686 (ppp) cc_final: 0.7398 (ppp) REVERT: j 16 ASP cc_start: 0.8800 (p0) cc_final: 0.7361 (t0) REVERT: j 49 MET cc_start: 0.7674 (mtt) cc_final: 0.7431 (mtt) REVERT: k 1 MET cc_start: 0.9575 (tpp) cc_final: 0.9216 (tpp) REVERT: k 58 PHE cc_start: 0.0410 (t80) cc_final: 0.0097 (t80) REVERT: l 67 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8515 (m-10) outliers start: 98 outliers final: 75 residues processed: 410 average time/residue: 0.4019 time to fit residues: 283.7666 Evaluate side-chains 412 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 328 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 64 ASN Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 234 MET Chi-restraints excluded: chain a residue 261 ASP Chi-restraints excluded: chain a residue 304 MET Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 507 VAL Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 650 GLN Chi-restraints excluded: chain a residue 658 LEU Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 856 THR Chi-restraints excluded: chain a residue 863 VAL Chi-restraints excluded: chain a residue 864 ILE Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1107 VAL Chi-restraints excluded: chain a residue 1116 LEU Chi-restraints excluded: chain a residue 1195 LEU Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1232 ASN Chi-restraints excluded: chain a residue 1318 THR Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 179 CYS Chi-restraints excluded: chain b residue 466 TRP Chi-restraints excluded: chain b residue 539 LEU Chi-restraints excluded: chain b residue 597 MET Chi-restraints excluded: chain b residue 651 LEU Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 694 ASP Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 840 ILE Chi-restraints excluded: chain b residue 870 ILE Chi-restraints excluded: chain b residue 1023 VAL Chi-restraints excluded: chain b residue 1028 GLU Chi-restraints excluded: chain b residue 1099 VAL Chi-restraints excluded: chain b residue 1147 LEU Chi-restraints excluded: chain b residue 1156 ASP Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1166 CYS Chi-restraints excluded: chain b residue 1196 ILE Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain c residue 238 ILE Chi-restraints excluded: chain d residue 165 GLN Chi-restraints excluded: chain e residue 5 ASN Chi-restraints excluded: chain e residue 202 SER Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 103 MET Chi-restraints excluded: chain f residue 133 VAL Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 ASP Chi-restraints excluded: chain g residue 163 ILE Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain j residue 52 THR Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain l residue 31 CYS Chi-restraints excluded: chain l residue 44 ASP Chi-restraints excluded: chain l residue 67 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 235 optimal weight: 30.0000 chunk 378 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 397 optimal weight: 0.0170 chunk 365 optimal weight: 10.0000 chunk 316 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b1179 GLN ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34167 Z= 0.230 Angle : 0.734 14.505 46545 Z= 0.373 Chirality : 0.044 0.232 5247 Planarity : 0.004 0.051 5704 Dihedral : 16.806 177.763 5419 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 2.65 % Allowed : 22.58 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3912 helix: 0.77 (0.15), residues: 1304 sheet: -0.96 (0.22), residues: 559 loop : -2.12 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 185 HIS 0.009 0.001 HIS g 158 PHE 0.056 0.002 PHE d 151 TYR 0.028 0.001 TYR b 994 ARG 0.007 0.000 ARG f 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 341 time to evaluate : 3.829 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: a 108 MET cc_start: 0.8845 (pmm) cc_final: 0.8383 (pmm) REVERT: a 122 MET cc_start: 0.9220 (pmm) cc_final: 0.8997 (pmm) REVERT: a 229 SER cc_start: 0.9345 (t) cc_final: 0.8831 (p) REVERT: a 234 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8603 (ttt) REVERT: a 260 ASP cc_start: 0.7735 (m-30) cc_final: 0.7525 (m-30) REVERT: a 261 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7236 (t0) REVERT: a 304 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8890 (tpp) REVERT: a 455 MET cc_start: 0.7545 (pmm) cc_final: 0.6909 (pmm) REVERT: a 456 MET cc_start: 0.8599 (mpp) cc_final: 0.7678 (mpp) REVERT: a 474 VAL cc_start: 0.9598 (t) cc_final: 0.9235 (p) REVERT: a 515 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8581 (tm-30) REVERT: a 521 MET cc_start: 0.9063 (mmm) cc_final: 0.8279 (mmm) REVERT: a 605 MET cc_start: 0.6905 (tpp) cc_final: 0.6587 (tpp) REVERT: a 708 MET cc_start: 0.6816 (pmm) cc_final: 0.6568 (pmm) REVERT: a 760 GLN cc_start: 0.9080 (mt0) cc_final: 0.8877 (mt0) REVERT: a 826 ASP cc_start: 0.8863 (t70) cc_final: 0.8661 (t70) REVERT: a 864 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.8946 (tp) REVERT: a 1116 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8267 (pp) REVERT: a 1317 MET cc_start: 0.8728 (tmm) cc_final: 0.8392 (tmm) REVERT: a 1375 MET cc_start: 0.9150 (tmm) cc_final: 0.8805 (tmm) REVERT: a 1400 CYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8615 (p) REVERT: a 1421 CYS cc_start: 0.8064 (t) cc_final: 0.7631 (p) REVERT: a 1426 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8788 (mm-30) REVERT: b 239 GLU cc_start: 0.8856 (tp30) cc_final: 0.8342 (tm-30) REVERT: b 412 LEU cc_start: 0.9159 (mt) cc_final: 0.8852 (mt) REVERT: b 542 MET cc_start: 0.8882 (mtp) cc_final: 0.7381 (mtt) REVERT: b 747 MET cc_start: 0.8711 (mmp) cc_final: 0.7710 (mmp) REVERT: b 834 ASN cc_start: 0.8235 (p0) cc_final: 0.7900 (m110) REVERT: b 1021 MET cc_start: 0.8061 (mmt) cc_final: 0.7676 (mmt) REVERT: b 1111 MET cc_start: 0.8763 (tpp) cc_final: 0.8561 (tpp) REVERT: b 1208 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7848 (pmm) REVERT: c 58 LEU cc_start: 0.8826 (mt) cc_final: 0.8028 (tp) REVERT: e 93 MET cc_start: 0.9301 (ppp) cc_final: 0.9061 (ppp) REVERT: e 114 ASN cc_start: 0.9118 (m-40) cc_final: 0.8481 (m110) REVERT: e 121 MET cc_start: 0.9761 (tpp) cc_final: 0.9553 (tpp) REVERT: f 103 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8154 (tmm) REVERT: f 112 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8953 (mp0) REVERT: g 64 THR cc_start: 0.9027 (t) cc_final: 0.8823 (p) REVERT: g 69 GLU cc_start: 0.8003 (tp30) cc_final: 0.7664 (tt0) REVERT: g 148 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7421 (mm-30) REVERT: h 97 MET cc_start: 0.7242 (tpt) cc_final: 0.6443 (tpp) REVERT: j 16 ASP cc_start: 0.8799 (p0) cc_final: 0.7309 (t0) REVERT: j 49 MET cc_start: 0.7676 (mtt) cc_final: 0.7434 (mtt) REVERT: k 1 MET cc_start: 0.9582 (tpp) cc_final: 0.9232 (tpp) outliers start: 92 outliers final: 74 residues processed: 410 average time/residue: 0.3978 time to fit residues: 281.5759 Evaluate side-chains 418 residues out of total 3484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 336 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 64 ASN Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 234 MET Chi-restraints excluded: chain a residue 261 ASP Chi-restraints excluded: chain a residue 304 MET Chi-restraints excluded: chain a residue 333 GLU Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 501 LEU Chi-restraints excluded: chain a residue 507 VAL Chi-restraints excluded: chain a residue 524 VAL Chi-restraints excluded: chain a residue 650 GLN Chi-restraints excluded: chain a residue 658 LEU Chi-restraints excluded: chain a residue 762 SER Chi-restraints excluded: chain a residue 831 THR Chi-restraints excluded: chain a residue 841 LEU Chi-restraints excluded: chain a residue 856 THR Chi-restraints excluded: chain a residue 863 VAL Chi-restraints excluded: chain a residue 864 ILE Chi-restraints excluded: chain a residue 965 GLN Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1107 VAL Chi-restraints excluded: chain a residue 1116 LEU Chi-restraints excluded: chain a residue 1195 LEU Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1318 THR Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1355 VAL Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1382 THR Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 179 CYS Chi-restraints excluded: chain b residue 466 TRP Chi-restraints excluded: chain b residue 539 LEU Chi-restraints excluded: chain b residue 603 LEU Chi-restraints excluded: chain b residue 651 LEU Chi-restraints excluded: chain b residue 684 LEU Chi-restraints excluded: chain b residue 694 ASP Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 840 ILE Chi-restraints excluded: chain b residue 870 ILE Chi-restraints excluded: chain b residue 1023 VAL Chi-restraints excluded: chain b residue 1028 GLU Chi-restraints excluded: chain b residue 1099 VAL Chi-restraints excluded: chain b residue 1147 LEU Chi-restraints excluded: chain b residue 1156 ASP Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1166 CYS Chi-restraints excluded: chain b residue 1180 PHE Chi-restraints excluded: chain b residue 1196 ILE Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 145 CYS Chi-restraints excluded: chain c residue 238 ILE Chi-restraints excluded: chain d residue 165 GLN Chi-restraints excluded: chain e residue 202 SER Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 103 MET Chi-restraints excluded: chain f residue 133 VAL Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 55 ASP Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain j residue 52 THR Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain l residue 31 CYS Chi-restraints excluded: chain l residue 44 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 251 optimal weight: 4.9990 chunk 337 optimal weight: 10.0000 chunk 96 optimal weight: 0.2980 chunk 291 optimal weight: 0.1980 chunk 46 optimal weight: 0.0770 chunk 87 optimal weight: 3.9990 chunk 317 optimal weight: 9.9990 chunk 132 optimal weight: 0.0010 chunk 325 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 776 GLN ** b 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b1179 GLN ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** 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 = 0.3653 r_free = 0.3653 target = 0.077503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.052445 restraints weight = 127449.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.054589 restraints weight = 59251.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.056032 restraints weight = 36605.956| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34167 Z= 0.187 Angle : 0.743 16.177 46545 Z= 0.370 Chirality : 0.044 0.231 5247 Planarity : 0.004 0.050 5704 Dihedral : 16.691 177.335 5419 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 2.05 % Allowed : 23.24 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3912 helix: 0.81 (0.15), residues: 1301 sheet: -0.75 (0.23), residues: 530 loop : -2.07 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP k 109 HIS 0.007 0.001 HIS g 158 PHE 0.052 0.002 PHE d 151 TYR 0.023 0.001 TYR b 994 ARG 0.009 0.000 ARG h 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7028.83 seconds wall clock time: 129 minutes 26.30 seconds (7766.30 seconds total)